[med-svn] r1461 - in trunk/packages: . biofox biofox/trunk biofox/trunk/debian biosquid biosquid/trunk biosquid/trunk/debian biosquid/trunk/debian/patches gdpc gdpc/trunk gdpc/trunk/debian gdpc/trunk/debian/patches gff2aplot gff2aplot/trunk gff2aplot/trunk/debian gff2aplot/trunk/debian/patches gff2ps gff2ps/trunk gff2ps/trunk/debian gff2ps/trunk/debian/patches gff2ps/trunk/debian/wrapper raster3d raster3d/trunk raster3d/trunk/debian raster3d/trunk/debian/patches raster3d/trunk/debian/wrappers
naoliv at alioth.debian.org
naoliv at alioth.debian.org
Sun Feb 24 03:33:38 UTC 2008
Author: naoliv
Date: 2008-02-24 03:33:37 +0000 (Sun, 24 Feb 2008)
New Revision: 1461
Added:
trunk/packages/biofox/
trunk/packages/biofox/branches/
trunk/packages/biofox/tags/
trunk/packages/biofox/trunk/
trunk/packages/biofox/trunk/debian/
trunk/packages/biofox/trunk/debian/README.Debian
trunk/packages/biofox/trunk/debian/Uninstall
trunk/packages/biofox/trunk/debian/changelog
trunk/packages/biofox/trunk/debian/chrome.d
trunk/packages/biofox/trunk/debian/chrome.manifest
trunk/packages/biofox/trunk/debian/compat
trunk/packages/biofox/trunk/debian/control
trunk/packages/biofox/trunk/debian/copyright
trunk/packages/biofox/trunk/debian/dirs
trunk/packages/biofox/trunk/debian/links
trunk/packages/biofox/trunk/debian/postinst
trunk/packages/biofox/trunk/debian/postrm
trunk/packages/biofox/trunk/debian/preinst
trunk/packages/biofox/trunk/debian/rules
trunk/packages/biofox/trunk/debian/watch
trunk/packages/biosquid/
trunk/packages/biosquid/branches/
trunk/packages/biosquid/tags/
trunk/packages/biosquid/trunk/
trunk/packages/biosquid/trunk/debian/
trunk/packages/biosquid/trunk/debian/biosquid-dev.README.Debian
trunk/packages/biosquid/trunk/debian/biosquid-dev.install
trunk/packages/biosquid/trunk/debian/biosquid.README.Debian
trunk/packages/biosquid/trunk/debian/biosquid.install
trunk/packages/biosquid/trunk/debian/biosquid.manpages
trunk/packages/biosquid/trunk/debian/changelog
trunk/packages/biosquid/trunk/debian/compalign.1
trunk/packages/biosquid/trunk/debian/compat
trunk/packages/biosquid/trunk/debian/control
trunk/packages/biosquid/trunk/debian/copyright
trunk/packages/biosquid/trunk/debian/patches/
trunk/packages/biosquid/trunk/debian/patches/Makefile.in.patch
trunk/packages/biosquid/trunk/debian/patches/afetch.man.patch
trunk/packages/biosquid/trunk/debian/patches/alistat.man.patch
trunk/packages/biosquid/trunk/debian/patches/compstruct.man.patch
trunk/packages/biosquid/trunk/debian/patches/seqstat.man.patch
trunk/packages/biosquid/trunk/debian/patches/sfetch.man.patch
trunk/packages/biosquid/trunk/debian/patches/shuffle.man.patch
trunk/packages/biosquid/trunk/debian/patches/sindex.man.patch
trunk/packages/biosquid/trunk/debian/patches/sreformat.man.patch
trunk/packages/biosquid/trunk/debian/revcomp.1
trunk/packages/biosquid/trunk/debian/rules
trunk/packages/biosquid/trunk/debian/seqsplit.1
trunk/packages/biosquid/trunk/debian/stranslate.1
trunk/packages/biosquid/trunk/debian/watch
trunk/packages/biosquid/trunk/debian/weight.1
trunk/packages/gdpc/
trunk/packages/gdpc/branches/
trunk/packages/gdpc/tags/
trunk/packages/gdpc/trunk/
trunk/packages/gdpc/trunk/debian/
trunk/packages/gdpc/trunk/debian/changelog
trunk/packages/gdpc/trunk/debian/compat
trunk/packages/gdpc/trunk/debian/control
trunk/packages/gdpc/trunk/debian/copyright
trunk/packages/gdpc/trunk/debian/dirs
trunk/packages/gdpc/trunk/debian/gdpc-examples.dirs
trunk/packages/gdpc/trunk/debian/gdpc-examples.install
trunk/packages/gdpc/trunk/debian/gdpc.1
trunk/packages/gdpc/trunk/debian/gdpc.README.Debian
trunk/packages/gdpc/trunk/debian/gdpc.desktop
trunk/packages/gdpc/trunk/debian/gdpc.install
trunk/packages/gdpc/trunk/debian/menu
trunk/packages/gdpc/trunk/debian/patches/
trunk/packages/gdpc/trunk/debian/patches/Makefile.diff
trunk/packages/gdpc/trunk/debian/rules
trunk/packages/gdpc/trunk/debian/watch
trunk/packages/gff2aplot/
trunk/packages/gff2aplot/branches/
trunk/packages/gff2aplot/tags/
trunk/packages/gff2aplot/trunk/
trunk/packages/gff2aplot/trunk/debian/
trunk/packages/gff2aplot/trunk/debian/ali2gff.1
trunk/packages/gff2aplot/trunk/debian/blat2gff.1
trunk/packages/gff2aplot/trunk/debian/changelog
trunk/packages/gff2aplot/trunk/debian/compat
trunk/packages/gff2aplot/trunk/debian/control
trunk/packages/gff2aplot/trunk/debian/copyright
trunk/packages/gff2aplot/trunk/debian/dirs
trunk/packages/gff2aplot/trunk/debian/docs
trunk/packages/gff2aplot/trunk/debian/gff2aplot.1
trunk/packages/gff2aplot/trunk/debian/parseblast.1
trunk/packages/gff2aplot/trunk/debian/patches/
trunk/packages/gff2aplot/trunk/debian/patches/01-makefile.diff
trunk/packages/gff2aplot/trunk/debian/patches/02-blat2gff.diff
trunk/packages/gff2aplot/trunk/debian/patches/03-parseblast.diff
trunk/packages/gff2aplot/trunk/debian/rules
trunk/packages/gff2aplot/trunk/debian/sim2gff.1
trunk/packages/gff2aplot/trunk/debian/watch
trunk/packages/gff2ps/
trunk/packages/gff2ps/branches/
trunk/packages/gff2ps/tags/
trunk/packages/gff2ps/trunk/
trunk/packages/gff2ps/trunk/debian/
trunk/packages/gff2ps/trunk/debian/README.Debian
trunk/packages/gff2ps/trunk/debian/changelog
trunk/packages/gff2ps/trunk/debian/compat
trunk/packages/gff2ps/trunk/debian/control
trunk/packages/gff2ps/trunk/debian/copyright
trunk/packages/gff2ps/trunk/debian/dirs
trunk/packages/gff2ps/trunk/debian/gff2ps.1
trunk/packages/gff2ps/trunk/debian/install
trunk/packages/gff2ps/trunk/debian/linda.override
trunk/packages/gff2ps/trunk/debian/manpages
trunk/packages/gff2ps/trunk/debian/patches/
trunk/packages/gff2ps/trunk/debian/patches/01-gff2ps_v0.98d.diff
trunk/packages/gff2ps/trunk/debian/rules
trunk/packages/gff2ps/trunk/debian/watch
trunk/packages/gff2ps/trunk/debian/wrapper/
trunk/packages/gff2ps/trunk/debian/wrapper/gff2ps
trunk/packages/raster3d/
trunk/packages/raster3d/branches/
trunk/packages/raster3d/tags/
trunk/packages/raster3d/trunk/
trunk/packages/raster3d/trunk/debian/
trunk/packages/raster3d/trunk/debian/changelog
trunk/packages/raster3d/trunk/debian/compat
trunk/packages/raster3d/trunk/debian/control
trunk/packages/raster3d/trunk/debian/copyright
trunk/packages/raster3d/trunk/debian/install
trunk/packages/raster3d/trunk/debian/patches/
trunk/packages/raster3d/trunk/debian/patches/BUGS.diff
trunk/packages/raster3d/trunk/debian/patches/Makefile.diff
trunk/packages/raster3d/trunk/debian/patches/Makefile.template.diff
trunk/packages/raster3d/trunk/debian/patches/example1.script.diff
trunk/packages/raster3d/trunk/debian/patches/example2.script.diff
trunk/packages/raster3d/trunk/debian/patches/example2.sgi.diff
trunk/packages/raster3d/trunk/debian/patches/example3.script.diff
trunk/packages/raster3d/trunk/debian/patches/example4.script.diff
trunk/packages/raster3d/trunk/debian/patches/example5.script.diff
trunk/packages/raster3d/trunk/debian/patches/example6.script.diff
trunk/packages/raster3d/trunk/debian/patches/example7.script.diff
trunk/packages/raster3d/trunk/debian/patches/example8.script.diff
trunk/packages/raster3d/trunk/debian/patches/example9.script.diff
trunk/packages/raster3d/trunk/debian/patches/msms_example.script.diff
trunk/packages/raster3d/trunk/debian/patches/r3d_objects.man.diff
trunk/packages/raster3d/trunk/debian/patches/raster3d-2.7d-gcc4-gentoo.patch
trunk/packages/raster3d/trunk/debian/patches/raster3d.man.diff
trunk/packages/raster3d/trunk/debian/patches/render.man.diff
trunk/packages/raster3d/trunk/debian/patches/rods.man.diff
trunk/packages/raster3d/trunk/debian/raster3d-doc.README.Debian
trunk/packages/raster3d/trunk/debian/raster3d-doc.doc-base
trunk/packages/raster3d/trunk/debian/raster3d-doc.install
trunk/packages/raster3d/trunk/debian/raster3d-doc.links
trunk/packages/raster3d/trunk/debian/raster3d.README.Debian
trunk/packages/raster3d/trunk/debian/raster3d.docs
trunk/packages/raster3d/trunk/debian/raster3d.manpages
trunk/packages/raster3d/trunk/debian/rings3d.1
trunk/packages/raster3d/trunk/debian/rules
trunk/packages/raster3d/trunk/debian/watch
trunk/packages/raster3d/trunk/debian/wrappers/
trunk/packages/raster3d/trunk/debian/wrappers/normal3d
trunk/packages/raster3d/trunk/debian/wrappers/render
Log:
mass commit party!
Added: trunk/packages/biofox/trunk/debian/README.Debian
===================================================================
--- trunk/packages/biofox/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/biofox/trunk/debian/README.Debian 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,28 @@
+biofox for Debian
+---------------------------------
+
+You need to restart your browser in order the changes take effect.
+Also, Biofox is a sidebar.
+
+To access it on Iceweasel, you can press Ctrl+Shift+F or go to
+View, Sidebar, and choose bioFOX.
+Ctrl+Shift+F may not work on some systems. This is a known issue and
+upstream author is aware of it.
+
+On Iceape, you can access bioFOX pressing F9 tho show the sidebar and
+select bioFOX from the list. You can also access the sidebar through
+View, Show/Hide, and choose Sidebar.
+
+Biofox works basically with a selected text inside Iceweasel or Iceape.
+Clicking on a function of the sidebar and having a select text, Biofox
+will perform this function on the text.
+
+For example, you can have a genome sequence selected and select blastn, to
+perform a similarity search.
+
+A new window will open, presenting the desired result.
+
+More informations can be obtained from bioFOX homepage:
+http://schematron.unl.edu/biofox/
+
+ -- Nelson A. de Oliveira <naoliv at debian.org> Sat, 23 Feb 2008 15:11:41 -0300
Added: trunk/packages/biofox/trunk/debian/Uninstall
===================================================================
--- trunk/packages/biofox/trunk/debian/Uninstall (rev 0)
+++ trunk/packages/biofox/trunk/debian/Uninstall 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,3 @@
+register global package biofox
+register global skin classic/1.0
+register global locale en-US
Added: trunk/packages/biofox/trunk/debian/changelog
===================================================================
--- trunk/packages/biofox/trunk/debian/changelog (rev 0)
+++ trunk/packages/biofox/trunk/debian/changelog 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,81 @@
+biofox (1.1.4-3) unstable; urgency=low
+
+ * Remove dependencies on transition packages (Closes: #406804);
+ * Updated Standards-Version;
+ * Changed Maintainer to the Debian-Med Packaging Team;
+ * Added new Homepage field;
+ * Added Vcs-* fields.
+
+ -- Nelson A. de Oliveira <naoliv at debian.org> Sat, 23 Feb 2008 15:11:41 -0300
+
+biofox (1.1.4-2) unstable; urgency=low
+
+ * Firefox -> Iceweasel!
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com> Tue, 21 Nov 2006 13:59:36 -0200
+
+biofox (1.1.4-1) unstable; urgency=low
+
+ * New upstream release:
+ - Added support for Firefox 2.0;
+ - Added KEGG;
+ - One-click workspace button.
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com> Wed, 25 Oct 2006 17:24:43 -0300
+
+biofox (1.1.2+0-1) unstable; urgency=medium
+
+ * Using a new .orig.tar.gz file, provided by upstream author, instead using
+ a .xpi file. Also, BioFOX now contains a new logo (the old one was not
+ allowed to be distributed);
+ * Bumped Standards-Version to 3.7.2 (no changes needed);
+ * Updated for Firefox 1.5;
+ * Added "firefox |" on Depends of debian/control;
+ * Added a space before Homepage: on debian/control;
+ * Changed to debhelper compatibility level 5.
+ * Updated debian/copyright file;
+ * Medium Urgency since BioFOX on testing is not functional with Firefox 1.5
+ and also contains a non-free image.
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com> Wed, 10 May 2006 22:00:05 -0300
+
+biofox (1.1.2-1) unstable; urgency=low
+
+ * New upstream version:
+ - Biofox is now compatible with new versions of Firefox including the
+ 1.5 beta.
+ * debian/control: removed versioned depends on mozilla-firefox.
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com> Tue, 15 Nov 2005 15:27:48 -0200
+
+biofox (1.1-2) unstable; urgency=low
+
+ * Removing transitional package mozilla-firefox-biofox, since mozilla-biofox
+ has reached testing.
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com> Mon, 17 Oct 2005 09:24:03 -0200
+
+biofox (1.1-1) unstable; urgency=low
+
+ [Nelson A. de Oliveira]
+ * New upstream version:
+ - Added Clustalw alignment;
+ - Added fasta format support for analyzing multiple sequences;
+ - Added select and search pubmed/scirus.
+ * Renamed source package, since "biofox" is the original name used by
+ upstream author (correcting my mistake in using "mozilla-firefox-biofox");
+ * Biofox can now be used on Mozilla Firefox and Mozilla Suite:
+ - Depends: mozilla-firefox | mozilla-browser.
+ * mozilla-firefox-biofox is now a transitional package, to allow smooth
+ upgrade to the new mozilla-biofox;
+ * Updated README.Debian, README.source, watch file, postinst and postrm;
+ * Updated Standards-Version to 3.6.2.1 (no changes needed).
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com> Tue, 20 Sep 2005 19:14:18 -0300
+
+mozilla-firefox-biofox (1.0.1-1) unstable; urgency=low
+
+ * Initial release (Closes: #301673).
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com> Sun, 22 May 2005 00:55:03 -0300
+
Added: trunk/packages/biofox/trunk/debian/chrome.d
===================================================================
--- trunk/packages/biofox/trunk/debian/chrome.d (rev 0)
+++ trunk/packages/biofox/trunk/debian/chrome.d 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,3 @@
+content,install,url,jar:resource:/chrome/biofox.jar!/content/
+content,install,url,jar:resource:/chrome/biofox.jar!/locale/en-US/
+content,install,url,jar:resource:/chrome/biofox.jar!/skin/classic/biofox/
Added: trunk/packages/biofox/trunk/debian/chrome.manifest
===================================================================
--- trunk/packages/biofox/trunk/debian/chrome.manifest (rev 0)
+++ trunk/packages/biofox/trunk/debian/chrome.manifest 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,8 @@
+
+overlay chrome://navigator/content/navigator.xul chrome://biofox/content/biofoxoverlay.xul
+overlay chrome://communicator/content/pref/preftree.xul chrome://biofox/content/biofox-pref.xul
+overlay chrome://communicator/content/tasksOverlay.xul chrome://biofox/content/biofoxoverlay.xul
+overlay chrome://browser/content/browser.xul chrome://biofox/content/biofoxoverlay.xul
+content biofox jar:chrome/biofox.jar!/content/
+
+skin biofox classic/1.0 jar:chrome/biofox.jar!/skin/classic/biofox/
Added: trunk/packages/biofox/trunk/debian/compat
===================================================================
--- trunk/packages/biofox/trunk/debian/compat (rev 0)
+++ trunk/packages/biofox/trunk/debian/compat 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1 @@
+5
Added: trunk/packages/biofox/trunk/debian/control
===================================================================
--- trunk/packages/biofox/trunk/debian/control (rev 0)
+++ trunk/packages/biofox/trunk/debian/control 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,30 @@
+Source: biofox
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Nelson A. de Oliveira <naoliv at debian.org>
+Build-Depends: cdbs, debhelper (>= 5)
+Build-Depends-Indep: zip
+Standards-Version: 3.7.3
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/biofox/trunk/
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/biofox/trunk/
+Homepage: http://schematron.unl.edu/biofox/
+
+Package: mozilla-biofox
+Architecture: all
+Depends: iceweasel | iceape
+Description: extension of bioinformatics tools to Iceape and Iceweasel browsers
+ Code bioFOX aims at implementing various bioinformatics tools as an extension
+ on the Iceape and Iceweasel browsers. Analysis of your favorite gene(s)
+ usually require(s) retrieving it from a database like NCBI or Swiss-Prot and
+ then performing one or more tasks including but not limited to:
+ .
+ * Translation of a nucleotide sequence;
+ * Blast search (eg. blastn, blastp etc.) of the desired nucleotide/protein
+ sequence;
+ * Calculation of properties (like PI, charge, molecular weight, AT/GC content
+ etc.) of a protein/nucleotide sequence;
+ * Conversion between formats (Genbank, Fasta, Swiss-Prot etc.);
+ * Prediction of sequence for sub-cellular localization (PREDOTAR, TargetP,
+ pSORT etc).
Added: trunk/packages/biofox/trunk/debian/copyright
===================================================================
--- trunk/packages/biofox/trunk/debian/copyright (rev 0)
+++ trunk/packages/biofox/trunk/debian/copyright 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,488 @@
+This package was debianized by Adrian Mastronardi <amastronardi at gmail.com> and
+Nelson A. de Oliveira <naoliv at gmail.com> on Sun, 22 May 2005 00:55:03 -0300.
+
+It was downloaded from http://www.mozdev.org/source/browse/biofox/downloads/
+
+Copyright (C) 2005-2006 Saleem Mohammed <saleem.m at gmail.com>
+
+License:
+
+This software is released under MPL/GPL/LGPL.
+
+ MOZILLA PUBLIC LICENSE
+ Version 1.1
+
+ ---------------
+
+1. Definitions.
+
+ 1.0.1. "Commercial Use" means distribution or otherwise making the
+ Covered Code available to a third party.
+
+ 1.1. "Contributor" means each entity that creates or contributes to
+ the creation of Modifications.
+
+ 1.2. "Contributor Version" means the combination of the Original
+ Code, prior Modifications used by a Contributor, and the Modifications
+ made by that particular Contributor.
+
+ 1.3. "Covered Code" means the Original Code or Modifications or the
+ combination of the Original Code and Modifications, in each case
+ including portions thereof.
+
+ 1.4. "Electronic Distribution Mechanism" means a mechanism generally
+ accepted in the software development community for the electronic
+ transfer of data.
+
+ 1.5. "Executable" means Covered Code in any form other than Source
+ Code.
+
+ 1.6. "Initial Developer" means the individual or entity identified
+ as the Initial Developer in the Source Code notice required by Exhibit
+ A.
+
+ 1.7. "Larger Work" means a work which combines Covered Code or
+ portions thereof with code not governed by the terms of this License.
+
+ 1.8. "License" means this document.
+
+ 1.8.1. "Licensable" means having the right to grant, to the maximum
+ extent possible, whether at the time of the initial grant or
+ subsequently acquired, any and all of the rights conveyed herein.
+
+ 1.9. "Modifications" means any addition to or deletion from the
+ substance or structure of either the Original Code or any previous
+ Modifications. When Covered Code is released as a series of files, a
+ Modification is:
+ A. Any addition to or deletion from the contents of a file
+ containing Original Code or previous Modifications.
+
+ B. Any new file that contains any part of the Original Code or
+ previous Modifications.
+
+ 1.10. "Original Code" means Source Code of computer software code
+ which is described in the Source Code notice required by Exhibit A as
+ Original Code, and which, at the time of its release under this
+ License is not already Covered Code governed by this License.
+
+ 1.10.1. "Patent Claims" means any patent claim(s), now owned or
+ hereafter acquired, including without limitation, method, process,
+ and apparatus claims, in any patent Licensable by grantor.
+
+ 1.11. "Source Code" means the preferred form of the Covered Code for
+ making modifications to it, including all modules it contains, plus
+ any associated interface definition files, scripts used to control
+ compilation and installation of an Executable, or source code
+ differential comparisons against either the Original Code or another
+ well known, available Covered Code of the Contributor's choice. The
+ Source Code can be in a compressed or archival form, provided the
+ appropriate decompression or de-archiving software is widely available
+ for no charge.
+
+ 1.12. "You" (or "Your") means an individual or a legal entity
+ exercising rights under, and complying with all of the terms of, this
+ License or a future version of this License issued under Section 6.1.
+ For legal entities, "You" includes any entity which controls, is
+ controlled by, or is under common control with You. For purposes of
+ this definition, "control" means (a) the power, direct or indirect,
+ to cause the direction or management of such entity, whether by
+ contract or otherwise, or (b) ownership of more than fifty percent
+ (50%) of the outstanding shares or beneficial ownership of such
+ entity.
+
+2. Source Code License.
+
+ 2.1. The Initial Developer Grant.
+ The Initial Developer hereby grants You a world-wide, royalty-free,
+ non-exclusive license, subject to third party intellectual property
+ claims:
+ (a) under intellectual property rights (other than patent or
+ trademark) Licensable by Initial Developer to use, reproduce,
+ modify, display, perform, sublicense and distribute the Original
+ Code (or portions thereof) with or without Modifications, and/or
+ as part of a Larger Work; and
+
+ (b) under Patents Claims infringed by the making, using or
+ selling of Original Code, to make, have made, use, practice,
+ sell, and offer for sale, and/or otherwise dispose of the
+ Original Code (or portions thereof).
+
+ (c) the licenses granted in this Section 2.1(a) and (b) are
+ effective on the date Initial Developer first distributes
+ Original Code under the terms of this License.
+
+ (d) Notwithstanding Section 2.1(b) above, no patent license is
+ granted: 1) for code that You delete from the Original Code; 2)
+ separate from the Original Code; or 3) for infringements caused
+ by: i) the modification of the Original Code or ii) the
+ combination of the Original Code with other software or devices.
+
+ 2.2. Contributor Grant.
+ Subject to third party intellectual property claims, each Contributor
+ hereby grants You a world-wide, royalty-free, non-exclusive license
+
+ (a) under intellectual property rights (other than patent or
+ trademark) Licensable by Contributor, to use, reproduce, modify,
+ display, perform, sublicense and distribute the Modifications
+ created by such Contributor (or portions thereof) either on an
+ unmodified basis, with other Modifications, as Covered Code
+ and/or as part of a Larger Work; and
+
+ (b) under Patent Claims infringed by the making, using, or
+ selling of Modifications made by that Contributor either alone
+ and/or in combination with its Contributor Version (or portions
+ of such combination), to make, use, sell, offer for sale, have
+ made, and/or otherwise dispose of: 1) Modifications made by that
+ Contributor (or portions thereof); and 2) the combination of
+ Modifications made by that Contributor with its Contributor
+ Version (or portions of such combination).
+
+ (c) the licenses granted in Sections 2.2(a) and 2.2(b) are
+ effective on the date Contributor first makes Commercial Use of
+ the Covered Code.
+
+ (d) Notwithstanding Section 2.2(b) above, no patent license is
+ granted: 1) for any code that Contributor has deleted from the
+ Contributor Version; 2) separate from the Contributor Version;
+ 3) for infringements caused by: i) third party modifications of
+ Contributor Version or ii) the combination of Modifications made
+ by that Contributor with other software (except as part of the
+ Contributor Version) or other devices; or 4) under Patent Claims
+ infringed by Covered Code in the absence of Modifications made by
+ that Contributor.
+
+3. Distribution Obligations.
+
+ 3.1. Application of License.
+ The Modifications which You create or to which You contribute are
+ governed by the terms of this License, including without limitation
+ Section 2.2. The Source Code version of Covered Code may be
+ distributed only under the terms of this License or a future version
+ of this License released under Section 6.1, and You must include a
+ copy of this License with every copy of the Source Code You
+ distribute. You may not offer or impose any terms on any Source Code
+ version that alters or restricts the applicable version of this
+ License or the recipients' rights hereunder. However, You may include
+ an additional document offering the additional rights described in
+ Section 3.5.
+
+ 3.2. Availability of Source Code.
+ Any Modification which You create or to which You contribute must be
+ made available in Source Code form under the terms of this License
+ either on the same media as an Executable version or via an accepted
+ Electronic Distribution Mechanism to anyone to whom you made an
+ Executable version available; and if made available via Electronic
+ Distribution Mechanism, must remain available for at least twelve (12)
+ months after the date it initially became available, or at least six
+ (6) months after a subsequent version of that particular Modification
+ has been made available to such recipients. You are responsible for
+ ensuring that the Source Code version remains available even if the
+ Electronic Distribution Mechanism is maintained by a third party.
+
+ 3.3. Description of Modifications.
+ You must cause all Covered Code to which You contribute to contain a
+ file documenting the changes You made to create that Covered Code and
+ the date of any change. You must include a prominent statement that
+ the Modification is derived, directly or indirectly, from Original
+ Code provided by the Initial Developer and including the name of the
+ Initial Developer in (a) the Source Code, and (b) in any notice in an
+ Executable version or related documentation in which You describe the
+ origin or ownership of the Covered Code.
+
+ 3.4. Intellectual Property Matters
+ (a) Third Party Claims.
+ If Contributor has knowledge that a license under a third party's
+ intellectual property rights is required to exercise the rights
+ granted by such Contributor under Sections 2.1 or 2.2,
+ Contributor must include a text file with the Source Code
+ distribution titled "LEGAL" which describes the claim and the
+ party making the claim in sufficient detail that a recipient will
+ know whom to contact. If Contributor obtains such knowledge after
+ the Modification is made available as described in Section 3.2,
+ Contributor shall promptly modify the LEGAL file in all copies
+ Contributor makes available thereafter and shall take other steps
+ (such as notifying appropriate mailing lists or newsgroups)
+ reasonably calculated to inform those who received the Covered
+ Code that new knowledge has been obtained.
+
+ (b) Contributor APIs.
+ If Contributor's Modifications include an application programming
+ interface and Contributor has knowledge of patent licenses which
+ are reasonably necessary to implement that API, Contributor must
+ also include this information in the LEGAL file.
+
+ (c) Representations.
+ Contributor represents that, except as disclosed pursuant to
+ Section 3.4(a) above, Contributor believes that Contributor's
+ Modifications are Contributor's original creation(s) and/or
+ Contributor has sufficient rights to grant the rights conveyed by
+ this License.
+
+ 3.5. Required Notices.
+ You must duplicate the notice in Exhibit A in each file of the Source
+ Code. If it is not possible to put such notice in a particular Source
+ Code file due to its structure, then You must include such notice in a
+ location (such as a relevant directory) where a user would be likely
+ to look for such a notice. If You created one or more Modification(s)
+ You may add your name as a Contributor to the notice described in
+ Exhibit A. You must also duplicate this License in any documentation
+ for the Source Code where You describe recipients' rights or ownership
+ rights relating to Covered Code. You may choose to offer, and to
+ charge a fee for, warranty, support, indemnity or liability
+ obligations to one or more recipients of Covered Code. However, You
+ may do so only on Your own behalf, and not on behalf of the Initial
+ Developer or any Contributor. You must make it absolutely clear than
+ any such warranty, support, indemnity or liability obligation is
+ offered by You alone, and You hereby agree to indemnify the Initial
+ Developer and every Contributor for any liability incurred by the
+ Initial Developer or such Contributor as a result of warranty,
+ support, indemnity or liability terms You offer.
+
+ 3.6. Distribution of Executable Versions.
+ You may distribute Covered Code in Executable form only if the
+ requirements of Section 3.1-3.5 have been met for that Covered Code,
+ and if You include a notice stating that the Source Code version of
+ the Covered Code is available under the terms of this License,
+ including a description of how and where You have fulfilled the
+ obligations of Section 3.2. The notice must be conspicuously included
+ in any notice in an Executable version, related documentation or
+ collateral in which You describe recipients' rights relating to the
+ Covered Code. You may distribute the Executable version of Covered
+ Code or ownership rights under a license of Your choice, which may
+ contain terms different from this License, provided that You are in
+ compliance with the terms of this License and that the license for the
+ Executable version does not attempt to limit or alter the recipient's
+ rights in the Source Code version from the rights set forth in this
+ License. If You distribute the Executable version under a different
+ license You must make it absolutely clear that any terms which differ
+ from this License are offered by You alone, not by the Initial
+ Developer or any Contributor. You hereby agree to indemnify the
+ Initial Developer and every Contributor for any liability incurred by
+ the Initial Developer or such Contributor as a result of any such
+ terms You offer.
+
+ 3.7. Larger Works.
+ You may create a Larger Work by combining Covered Code with other code
+ not governed by the terms of this License and distribute the Larger
+ Work as a single product. In such a case, You must make sure the
+ requirements of this License are fulfilled for the Covered Code.
+
+4. Inability to Comply Due to Statute or Regulation.
+
+ If it is impossible for You to comply with any of the terms of this
+ License with respect to some or all of the Covered Code due to
+ statute, judicial order, or regulation then You must: (a) comply with
+ the terms of this License to the maximum extent possible; and (b)
+ describe the limitations and the code they affect. Such description
+ must be included in the LEGAL file described in Section 3.4 and must
+ be included with all distributions of the Source Code. Except to the
+ extent prohibited by statute or regulation, such description must be
+ sufficiently detailed for a recipient of ordinary skill to be able to
+ understand it.
+
+5. Application of this License.
+
+ This License applies to code to which the Initial Developer has
+ attached the notice in Exhibit A and to related Covered Code.
+
+6. Versions of the License.
+
+ 6.1. New Versions.
+ Netscape Communications Corporation ("Netscape") may publish revised
+ and/or new versions of the License from time to time. Each version
+ will be given a distinguishing version number.
+
+ 6.2. Effect of New Versions.
+ Once Covered Code has been published under a particular version of the
+ License, You may always continue to use it under the terms of that
+ version. You may also choose to use such Covered Code under the terms
+ of any subsequent version of the License published by Netscape. No one
+ other than Netscape has the right to modify the terms applicable to
+ Covered Code created under this License.
+
+ 6.3. Derivative Works.
+ If You create or use a modified version of this License (which you may
+ only do in order to apply it to code which is not already Covered Code
+ governed by this License), You must (a) rename Your license so that
+ the phrases "Mozilla", "MOZILLAPL", "MOZPL", "Netscape",
+ "MPL", "NPL" or any confusingly similar phrase do not appear in your
+ license (except to note that your license differs from this License)
+ and (b) otherwise make it clear that Your version of the license
+ contains terms which differ from the Mozilla Public License and
+ Netscape Public License. (Filling in the name of the Initial
+ Developer, Original Code or Contributor in the notice described in
+ Exhibit A shall not of themselves be deemed to be modifications of
+ this License.)
+
+7. DISCLAIMER OF WARRANTY.
+
+ COVERED CODE IS PROVIDED UNDER THIS LICENSE ON AN "AS IS" BASIS,
+ WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
+ WITHOUT LIMITATION, WARRANTIES THAT THE COVERED CODE IS FREE OF
+ DEFECTS, MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE OR NON-INFRINGING.
+ THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE COVERED CODE
+ IS WITH YOU. SHOULD ANY COVERED CODE PROVE DEFECTIVE IN ANY RESPECT,
+ YOU (NOT THE INITIAL DEVELOPER OR ANY OTHER CONTRIBUTOR) ASSUME THE
+ COST OF ANY NECESSARY SERVICING, REPAIR OR CORRECTION. THIS DISCLAIMER
+ OF WARRANTY CONSTITUTES AN ESSENTIAL PART OF THIS LICENSE. NO USE OF
+ ANY COVERED CODE IS AUTHORIZED HEREUNDER EXCEPT UNDER THIS DISCLAIMER.
+
+8. TERMINATION.
+
+ 8.1. This License and the rights granted hereunder will terminate
+ automatically if You fail to comply with terms herein and fail to cure
+ such breach within 30 days of becoming aware of the breach. All
+ sublicenses to the Covered Code which are properly granted shall
+ survive any termination of this License. Provisions which, by their
+ nature, must remain in effect beyond the termination of this License
+ shall survive.
+
+ 8.2. If You initiate litigation by asserting a patent infringement
+ claim (excluding declatory judgment actions) against Initial Developer
+ or a Contributor (the Initial Developer or Contributor against whom
+ You file such action is referred to as "Participant") alleging that:
+
+ (a) such Participant's Contributor Version directly or indirectly
+ infringes any patent, then any and all rights granted by such
+ Participant to You under Sections 2.1 and/or 2.2 of this License
+ shall, upon 60 days notice from Participant terminate prospectively,
+ unless if within 60 days after receipt of notice You either: (i)
+ agree in writing to pay Participant a mutually agreeable reasonable
+ royalty for Your past and future use of Modifications made by such
+ Participant, or (ii) withdraw Your litigation claim with respect to
+ the Contributor Version against such Participant. If within 60 days
+ of notice, a reasonable royalty and payment arrangement are not
+ mutually agreed upon in writing by the parties or the litigation claim
+ is not withdrawn, the rights granted by Participant to You under
+ Sections 2.1 and/or 2.2 automatically terminate at the expiration of
+ the 60 day notice period specified above.
+
+ (b) any software, hardware, or device, other than such Participant's
+ Contributor Version, directly or indirectly infringes any patent, then
+ any rights granted to You by such Participant under Sections 2.1(b)
+ and 2.2(b) are revoked effective as of the date You first made, used,
+ sold, distributed, or had made, Modifications made by that
+ Participant.
+
+ 8.3. If You assert a patent infringement claim against Participant
+ alleging that such Participant's Contributor Version directly or
+ indirectly infringes any patent where such claim is resolved (such as
+ by license or settlement) prior to the initiation of patent
+ infringement litigation, then the reasonable value of the licenses
+ granted by such Participant under Sections 2.1 or 2.2 shall be taken
+ into account in determining the amount or value of any payment or
+ license.
+
+ 8.4. In the event of termination under Sections 8.1 or 8.2 above,
+ all end user license agreements (excluding distributors and resellers)
+ which have been validly granted by You or any distributor hereunder
+ prior to termination shall survive termination.
+
+9. LIMITATION OF LIABILITY.
+
+ UNDER NO CIRCUMSTANCES AND UNDER NO LEGAL THEORY, WHETHER TORT
+ (INCLUDING NEGLIGENCE), CONTRACT, OR OTHERWISE, SHALL YOU, THE INITIAL
+ DEVELOPER, ANY OTHER CONTRIBUTOR, OR ANY DISTRIBUTOR OF COVERED CODE,
+ OR ANY SUPPLIER OF ANY OF SUCH PARTIES, BE LIABLE TO ANY PERSON FOR
+ ANY INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES OF ANY
+ CHARACTER INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF GOODWILL,
+ WORK STOPPAGE, COMPUTER FAILURE OR MALFUNCTION, OR ANY AND ALL OTHER
+ COMMERCIAL DAMAGES OR LOSSES, EVEN IF SUCH PARTY SHALL HAVE BEEN
+ INFORMED OF THE POSSIBILITY OF SUCH DAMAGES. THIS LIMITATION OF
+ LIABILITY SHALL NOT APPLY TO LIABILITY FOR DEATH OR PERSONAL INJURY
+ RESULTING FROM SUCH PARTY'S NEGLIGENCE TO THE EXTENT APPLICABLE LAW
+ PROHIBITS SUCH LIMITATION. SOME JURISDICTIONS DO NOT ALLOW THE
+ EXCLUSION OR LIMITATION OF INCIDENTAL OR CONSEQUENTIAL DAMAGES, SO
+ THIS EXCLUSION AND LIMITATION MAY NOT APPLY TO YOU.
+
+10. U.S. GOVERNMENT END USERS.
+
+ The Covered Code is a "commercial item," as that term is defined in
+ 48 C.F.R. 2.101 (Oct. 1995), consisting of "commercial computer
+ software" and "commercial computer software documentation," as such
+ terms are used in 48 C.F.R. 12.212 (Sept. 1995). Consistent with 48
+ C.F.R. 12.212 and 48 C.F.R. 227.7202-1 through 227.7202-4 (June 1995),
+ all U.S. Government End Users acquire Covered Code with only those
+ rights set forth herein.
+
+11. MISCELLANEOUS.
+
+ This License represents the complete agreement concerning subject
+ matter hereof. If any provision of this License is held to be
+ unenforceable, such provision shall be reformed only to the extent
+ necessary to make it enforceable. This License shall be governed by
+ California law provisions (except to the extent applicable law, if
+ any, provides otherwise), excluding its conflict-of-law provisions.
+ With respect to disputes in which at least one party is a citizen of,
+ or an entity chartered or registered to do business in the United
+ States of America, any litigation relating to this License shall be
+ subject to the jurisdiction of the Federal Courts of the Northern
+ District of California, with venue lying in Santa Clara County,
+ California, with the losing party responsible for costs, including
+ without limitation, court costs and reasonable attorneys' fees and
+ expenses. The application of the United Nations Convention on
+ Contracts for the International Sale of Goods is expressly excluded.
+ Any law or regulation which provides that the language of a contract
+ shall be construed against the drafter shall not apply to this
+ License.
+
+12. RESPONSIBILITY FOR CLAIMS.
+
+ As between Initial Developer and the Contributors, each party is
+ responsible for claims and damages arising, directly or indirectly,
+ out of its utilization of rights under this License and You agree to
+ work with Initial Developer and Contributors to distribute such
+ responsibility on an equitable basis. Nothing herein is intended or
+ shall be deemed to constitute any admission of liability.
+
+13. MULTIPLE-LICENSED CODE.
+
+ Initial Developer may designate portions of the Covered Code as
+ "Multiple-Licensed". "Multiple-Licensed" means that the Initial
+ Developer permits you to utilize portions of the Covered Code under
+ Your choice of the NPL or the alternative licenses, if any, specified
+ by the Initial Developer in the file described in Exhibit A.
+
+EXHIBIT A -Mozilla Public License.
+
+ ``The contents of this file are subject to the Mozilla Public License
+ Version 1.1 (the "License"); you may not use this file except in
+ compliance with the License. You may obtain a copy of the License at
+ http://www.mozilla.org/MPL/
+
+ Software distributed under the License is distributed on an "AS IS"
+ basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the
+ License for the specific language governing rights and limitations
+ under the License.
+
+ The Original Code is ______________________________________.
+
+ The Initial Developer of the Original Code is ________________________.
+ Portions created by ______________________ are Copyright (C) ______
+ _______________________. All Rights Reserved.
+
+ Contributor(s): ______________________________________.
+
+ Alternatively, the contents of this file may be used under the terms
+ of the _____ license (the "[___] License"), in which case the
+ provisions of [______] License are applicable instead of those
+ above. If you wish to allow use of your version of this file only
+ under the terms of the [____] License and not to allow others to use
+ your version of this file under the MPL, indicate your decision by
+ deleting the provisions above and replace them with the notice and
+ other provisions required by the [___] License. If you do not delete
+ the provisions above, a recipient may use your version of this file
+ under either the MPL or the [___] License."
+
+ [NOTE: The text of this Exhibit A may differ slightly from the text of
+ the notices in the Source Code files of the Original Code. You should
+ use the text of this Exhibit A rather than the text found in the
+ Original Code Source Code for Your Modifications.]
+
+====================
+
+GPL and LGPL License:
+On Debian systems, the complete text of the GNU General
+Public License can be found in `/usr/share/common-licenses/GPL' and
+the complete text of the GNU Lesser General Public License can be
+found in `/usr/share/common-licenses/LGPL'.
Added: trunk/packages/biofox/trunk/debian/dirs
===================================================================
--- trunk/packages/biofox/trunk/debian/dirs (rev 0)
+++ trunk/packages/biofox/trunk/debian/dirs 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1 @@
+/usr/share/iceape/chrome
Added: trunk/packages/biofox/trunk/debian/links
===================================================================
--- trunk/packages/biofox/trunk/debian/links (rev 0)
+++ trunk/packages/biofox/trunk/debian/links 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,2 @@
+usr/lib/iceweasel/extensions/{fbfbf0bf-032e-427e-932d-0b000a34f168}/chrome/biofox.jar usr/share/iceape/chrome/biofox.jar
+usr/lib/iceweasel/extensions/{fbfbf0bf-032e-427e-932d-0b000a34f168}/chrome.d var/lib/iceape/chrome.d/50biofox
Added: trunk/packages/biofox/trunk/debian/postinst
===================================================================
--- trunk/packages/biofox/trunk/debian/postinst (rev 0)
+++ trunk/packages/biofox/trunk/debian/postinst 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,29 @@
+#! /bin/sh
+# postinst script for biofox
+
+set -e
+
+case "$1" in
+ configure)
+ if which update-iceape-chrome 2> /dev/null > /dev/null
+ then
+ update-iceape-chrome
+ fi
+ ;;
+
+ abort-upgrade|abort-remove|abort-deconfigure)
+
+ ;;
+
+ *)
+ echo "postinst called with unknown argument \`$1'" >&2
+ exit 1
+ ;;
+esac
+
+# dh_installdeb will replace this with shell code automatically
+# generated by other debhelper scripts.
+
+#DEBHELPER#
+
+exit 0
Added: trunk/packages/biofox/trunk/debian/postrm
===================================================================
--- trunk/packages/biofox/trunk/debian/postrm (rev 0)
+++ trunk/packages/biofox/trunk/debian/postrm 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,27 @@
+#! /bin/sh
+# postrm script for biofox
+
+set -e
+
+case "$1" in
+ remove|abort-install)
+ if which update-iceape-chrome 2> /dev/null > /dev/null
+ then
+ update-iceape-chrome
+ fi
+ ;;
+ purge|upgrade|failed-upgrade|abort-upgrade|disappear)
+ ;;
+
+ *)
+ echo "postrm called with unknown argument \`$1'" >&2
+ exit 1
+
+esac
+
+# dh_installdeb will replace this with shell code automatically
+# generated by other debhelper scripts.
+
+#DEBHELPER#
+
+exit 0
Added: trunk/packages/biofox/trunk/debian/preinst
===================================================================
--- trunk/packages/biofox/trunk/debian/preinst (rev 0)
+++ trunk/packages/biofox/trunk/debian/preinst 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,10 @@
+#!/bin/sh
+
+set -e
+
+if [ "$1" = upgrade ]; then
+ rm -rf /usr/share/mozilla-extensions/biofox/
+ rm -rf /usr/lib/iceweasel/extensions/\{fbfbf0bf-032e-427e-932d-0b000a34f168\}
+fi
+
+#DEBHELPER#
Added: trunk/packages/biofox/trunk/debian/rules
===================================================================
--- trunk/packages/biofox/trunk/debian/rules (rev 0)
+++ trunk/packages/biofox/trunk/debian/rules 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,22 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/rules/debhelper.mk
+
+DEB_DESTDIR := $(CURDIR)/debian/mozilla-biofox
+
+EXT_ID := {fbfbf0bf-032e-427e-932d-0b000a34f168}
+PLUGIN_DIR := $(DEB_DESTDIR)/usr/lib/iceweasel/extensions/$(EXT_ID)
+
+clean::
+ rm -f biofox.jar
+
+install/mozilla-biofox::
+ cd chrome/ && zip -9 -r ../biofox.jar content/ locale/ skin/ -x `find -name .DS_Store`
+ mkdir -p $(PLUGIN_DIR)/uninstall
+ mkdir $(PLUGIN_DIR)/chrome
+ install -m 644 debian/chrome.d $(PLUGIN_DIR)
+ install -m 644 debian/chrome.manifest $(PLUGIN_DIR)
+ install -m 644 debian/Uninstall $(PLUGIN_DIR)/uninstall/
+ install -m 644 install.rdf $(PLUGIN_DIR)
+ install -m 644 biofox.jar $(PLUGIN_DIR)/chrome/
+ echo "extension,$(EXT_ID)" > $(PLUGIN_DIR)/extensions.d
Property changes on: trunk/packages/biofox/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/biofox/trunk/debian/watch
===================================================================
--- trunk/packages/biofox/trunk/debian/watch (rev 0)
+++ trunk/packages/biofox/trunk/debian/watch 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,2 @@
+version=3
+http://downloads.mozdev.org/biofox/biofox-(.*).xpi
Added: trunk/packages/biosquid/trunk/debian/biosquid-dev.README.Debian
===================================================================
--- trunk/packages/biosquid/trunk/debian/biosquid-dev.README.Debian (rev 0)
+++ trunk/packages/biosquid/trunk/debian/biosquid-dev.README.Debian 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,7 @@
+biosquid-dev for Debian
+-----------------------
+
+ All the header files are installed on /usr/include/biosquid/ instead
+ being installed on /usr/include/
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com> Fri, 04 Aug 2006 17:53:28 -03000
Added: trunk/packages/biosquid/trunk/debian/biosquid-dev.install
===================================================================
--- trunk/packages/biosquid/trunk/debian/biosquid-dev.install (rev 0)
+++ trunk/packages/biosquid/trunk/debian/biosquid-dev.install 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,2 @@
+debian/tmp/include/* usr/include/biosquid/
+debian/tmp/lib/ usr/
Added: trunk/packages/biosquid/trunk/debian/biosquid.README.Debian
===================================================================
--- trunk/packages/biosquid/trunk/debian/biosquid.README.Debian (rev 0)
+++ trunk/packages/biosquid/trunk/debian/biosquid.README.Debian 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,13 @@
+biosquid for Debian
+-------------------
+
+ The original name of the package is "squid", but since there is already
+ a squid on the archive (a proxy cache) it was renamed to "biosquid", as
+ suggested by Sean Eddy, upstream author of the program.
+
+ Biosquid was compiled with LFS (Large File Support) enabled.
+
+ Also, the "translate" binary was renamed to "stranslate", avoiding
+ conflict with the binary of the same name, from the "translate" package.
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com> Fri, 04 Aug 2006 17:53:28 -03000
Added: trunk/packages/biosquid/trunk/debian/biosquid.install
===================================================================
--- trunk/packages/biosquid/trunk/debian/biosquid.install (rev 0)
+++ trunk/packages/biosquid/trunk/debian/biosquid.install 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,2 @@
+debian/tmp/bin/ usr/
+debian/tmp/share/ usr/
Added: trunk/packages/biosquid/trunk/debian/biosquid.manpages
===================================================================
--- trunk/packages/biosquid/trunk/debian/biosquid.manpages (rev 0)
+++ trunk/packages/biosquid/trunk/debian/biosquid.manpages 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,5 @@
+debian/compalign.1
+debian/revcomp.1
+debian/seqsplit.1
+debian/stranslate.1
+debian/weight.1
Added: trunk/packages/biosquid/trunk/debian/changelog
===================================================================
--- trunk/packages/biosquid/trunk/debian/changelog (rev 0)
+++ trunk/packages/biosquid/trunk/debian/changelog 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,20 @@
+biosquid (1.9g+cvs20050121-2) unstable; urgency=low
+
+ [ Andreas Tille ]
+ * Use Homepage tag control field instead of putting it into
+ long description (Closes: #466005).
+
+ [ Nelson A. de Oliveira ]
+ * Update watch file (Closes: #453579);
+ * Updated Standards-Version;
+ * Changed Maintainer to the Debian-Med Packaging Team;
+ * Added Vcs-* fields.
+
+ -- Nelson A. de Oliveira <naoliv at debian.org> Thu, 21 Feb 2008 22:41:01 -0300
+
+biosquid (1.9g+cvs20050121-1) unstable; urgency=low
+
+ * Initial release (Closes: #319945).
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com> Sat, 5 Aug 2006 01:03:52 -0300
+
Added: trunk/packages/biosquid/trunk/debian/compalign.1
===================================================================
--- trunk/packages/biosquid/trunk/debian/compalign.1 (rev 0)
+++ trunk/packages/biosquid/trunk/debian/compalign.1 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,76 @@
+.TH COMPALIGN 1 "Mon, 01 Aug 2005 15:28:08 -0300"
+.SH NAME
+compalign \- compare two multiple alignments
+.SH SYNOPSIS
+.B compalign
+.RI "[-options] <trusted-alignment> <test-alignment>"
+.SH DESCRIPTION
+.PP
+\fBcompalign\fP calculates the fractional "identity" between the trusted alignment and the test alignment. The two files must contain exactly the same sequences, in exactly the same order.
+.sp 1
+The identity of the multiple sequence alignments is defined as the averaged identity over all N(N-1)/2 pairwise alignments.
+.sp 1
+The fractional identity of two sets of pairwise alignments is in turn defined as follows (for aligned known sequences k1 and k2, and aligned test sequences t1 and t2):
+.sp 1
+.nf
+ matched columns / total columns
+
+ where total columns = the total number of columns in which there is
+ a valid (nongap) symbol in k1 or k2;
+
+ matched columns = the number of columns in which one of the
+ following is true:
+
+ k1 and k2 both have valid symbols at a given column; t1 and t2
+ have the same symbols aligned in a column of the t1/t2
+ alignment;
+
+ k1 has a symbol aligned to a gap in k2; that symbol in t1 is
+ also aligned to a gap;
+
+ k2 has a symbol aligned to a gap in k1; that symbol in t2 is
+ also aligned to a gap.
+
+.fi
+Because scores for all possible pairs are calculated, the algorithm is of order (N^2)L for N sequences of length L; large sequence sets will take a while.
+.SH OPTIONS
+Available options:
+.TP
+.B \-h
+Print short help and usage info.
+.TP
+.B \-c
+Only compare under marked #=CS consensus structure.
+.TP
+.B \-\-informat <s>
+Specify that both alignments are in format <s> (MSF, for instance).
+.TP
+.B \-\-quiet
+Suppress verbose header (used in regression testing).
+.SH SEE ALSO
+.BR afetch (1),
+.BR alistat (1),
+.BR compstruct (1),
+.BR revcomp (1),
+.BR seqsplit (1),
+.BR seqstat (1),
+.BR sfetch (1),
+.BR shuffle (1),
+.BR sindex (1),
+.BR sreformat (1),
+.BR stranslate (1),
+.BR weight (1).
+.br
+.SH AUTHOR
+.nf
+Sean Eddy
+HHMI/Department of Genetics
+Washington University School of Medicine
+4444 Forest Park Blvd., Box 8510
+St Louis, MO 63108 USA
+Phone: 1-314-362-7666
+FAX : 1-314-362-2157
+Email: eddy at genetics.wustl.edu
+.PP
+This manual page was written by Nelson A. de Oliveira <naoliv at gmail.com>,
+for the Debian project (but may be used by others).
Added: trunk/packages/biosquid/trunk/debian/compat
===================================================================
--- trunk/packages/biosquid/trunk/debian/compat (rev 0)
+++ trunk/packages/biosquid/trunk/debian/compat 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1 @@
+5
Added: trunk/packages/biosquid/trunk/debian/control
===================================================================
--- trunk/packages/biosquid/trunk/debian/control (rev 0)
+++ trunk/packages/biosquid/trunk/debian/control 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,37 @@
+Source: biosquid
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Nelson A. de Oliveira <naoliv at debian.org>
+Build-Depends: cdbs, debhelper (>= 5), autoconf, autotools-dev
+Standards-Version: 3.7.3
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/biosquid/trunk/
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/biosquid/trunk/
+Homepage: http://selab.wustl.edu/cgi-bin/selab.pl?mode=software
+
+Package: biosquid
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Conflicts: hmmer (<= 2.1.4)
+Recommends: hmmer (>> 2.1.4)
+Description: utilities for biological sequence analysis
+ SQUID is a library of C code functions for sequence analysis. It also
+ includes a number of small utility programs to convert, show statistics,
+ manipulate and do other functions on sequence files.
+ .
+ The original name of the package is "squid", but since there is already
+ a squid on the archive (a proxy cache), it was renamed to "biosquid".
+
+Package: biosquid-dev
+Section: devel
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: biosquid
+Description: headers and static library for biological sequence analysis
+ SQUID is a library of C code functions for sequence analysis. It also
+ includes a number of small utility programs to convert, show statistics,
+ manipulate and do other functions on sequence files.
+ .
+ The original name of the package is "squid", but since there is already
+ a squid on the archive (a proxy cache), it was renamed to "biosquid".
Added: trunk/packages/biosquid/trunk/debian/copyright
===================================================================
--- trunk/packages/biosquid/trunk/debian/copyright (rev 0)
+++ trunk/packages/biosquid/trunk/debian/copyright 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,43 @@
+This package was debianized by Nelson A. de Oliveira <naoliv at gmail.com> on
+Sun, 23 Oct 2005 01:04:17 -0200.
+
+It was downloaded from http://selab.wustl.edu/cgi-bin/selab.pl?mode=software
+
+Upstream Author: Sean Eddy <eddy at genetics.wustl.edu>
+
+Copyright (C) 1992-2005 Washington University School of Medicine
+All Rights Reserved
+
+This suite of programs is free software. You can redistribute it
+and/or modify it under the terms of the GNU General Public License as
+published by the Free Software Foundation; either version 2 of the
+License, or (at your option) any later version.
+
+In other words, you are free to modify, copy, or redistribute this
+source code and its documentation in any way you like, but you must
+distribute all derivative versions as free software under the same
+terms that I've provided my code to you (i.e. the GNU General Public
+License). This precludes any use of the code in proprietary or
+commercial software unless your source code is made freely available.
+
+If you wish to use SQUID code under a different Open Source license
+that's not compatible with the GPL (like the Artistic License, BSD
+license, or the Netscape Public License), please contact me
+(eddy at genetics.wustl.edu) for permission.
+
+Incorporation into commercial software under non-GPL terms is
+possible, by arranging a license with the Washington University School
+of Medicine Center for Technology Management (CTM). For this purpose,
+the CTM is authorized to negotiate on behalf of the Howard Hughes
+Medical Institute, the other copyright holder on the code. Certain
+third party code modules may have to be removed from a non-GPL
+distribution. Contact Tom Hagerty (HagertyT at otm.wustl.edu) in our
+Office of Technology Management to arrange non-GPL licensing terms.
+
+This software is distributed in the hope that it will be useful, but
+WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+General Public License for more details.
+
+On Debian systems, the complete text of the GNU General
+Public License can be found in `/usr/share/common-licenses/GPL'.
Added: trunk/packages/biosquid/trunk/debian/patches/Makefile.in.patch
===================================================================
--- trunk/packages/biosquid/trunk/debian/patches/Makefile.in.patch (rev 0)
+++ trunk/packages/biosquid/trunk/debian/patches/Makefile.in.patch 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,115 @@
+diff -Nur squid/Makefile.in squid.new/Makefile.in
+--- squid/Makefile.in 2006-07-30 18:39:11.000000000 -0300
++++ squid.new/Makefile.in 2006-08-04 18:03:03.000000000 -0300
+@@ -75,10 +75,12 @@
+
+ MANS = afetch\
+ alistat\
++ compstruct\
+ seqstat\
+ sfetch\
+ shuffle\
+- sreformat\
++ sindex\
++ sreformat
+
+ READMES = 00README INSTALL Makefile.in
+
+@@ -103,51 +105,80 @@
+ stopwatch.h\
+ vectorops.h
+
+-OBJS = a2m.o\
+- aligneval.o\
++COMMON_OBJS = \
++ a2m.o\
+ alignio.o\
+ clustal.o\
+- cluster.o\
+- dayhoff.o\
+- dirichlet.o\
+- eps.o\
+ file.o\
+ getopt.o\
+ gki.o\
+ hsregex.o\
+- iupac.o\
+ msa.o\
+ msf.o\
+ phylip.o\
+- revcomp.o\
+- rk.o\
+ selex.o\
+- seqencode.o\
+- shuffle.o\
+ sqerror.o\
+ sqio.o\
+ squidcore.o\
+ sre_ctype.o\
+- sre_math.o\
+ sre_random.o\
+- sre_stack.o\
+ sre_string.o\
+ ssi.o\
+ stockholm.o\
++ types.o\
++ vectorops.o
++
++OBJS = $(COMMON_OBJS)\
++ aligneval.o\
++ cluster.o\
++ dayhoff.o\
++ dirichlet.o\
++ eps.o\
++ iupac.o\
++ revcomp.o\
++ rk.o\
++ seqencode.o\
++ shuffle.o\
++ sre_math.o\
++ sre_stack.o\
+ stopwatch.o\
+ translate.o\
+- types.o\
+- vectorops.o\
+ weight.o\
+ wuss.o
+
++MAINS = afetch_main.o\
++ alistat_main.o\
++ compalign_main.o\
++ compstruct_main.o\
++ revcomp_main.o\
++ seqsplit_main.o\
++ seqstat_main.o\
++ sfetch_main.o\
++ shuffle_main.o\
++ sindex_main.o\
++ sreformat_main.o\
++ translate_main.o\
++ weight_main.o
++
+
+ ################################################################
+ # Targets that actually build the squid executables
+ all: $(PROGS) libsquid.a
+
+-$(PROGS): @EXEC_DEPENDENCY@ ${OBJS}
+- ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o $@ $@_main.o ${OBJS} ${PVMLIBS} ${LIBS}
++$(PROGS): @EXEC_DEPENDENCY@ ${OBJS} ${MAINS}
++ ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o afetch afetch_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS}
++ ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o alistat aligneval.o cluster.o sre_math.o sre_stack.o alistat_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS}
++ ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o compalign aligneval.o compalign_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS}
++ ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o compstruct sre_math.o sre_stack.o wuss.o compstruct_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS}
++ ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o revcomp revcomp.o shuffle.o revcomp_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS}
++ ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o seqsplit seqsplit_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS}
++ ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o seqstat seqstat_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS}
++ ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o sfetch revcomp.o shuffle.o sfetch_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS}
++ ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o shuffle iupac.o shuffle.o shuffle_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS}
++ ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o sindex sindex_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS}
++ ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o sreformat eps.o shuffle.o sre_stack.o wuss.o sreformat_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS}
++ ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o translate iupac.o revcomp.o shuffle.o sre_stack.o translate.o translate_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS}
++ ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o weight aligneval.o cluster.o iupac.o sre_math.o sre_stack.o weight.o weight_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS}
+
+ .c.o:
+ ${CC} ${CFLAGS} ${CPPFLAGS} ${PVMINCDIR} ${DEFS} -c $<
Added: trunk/packages/biosquid/trunk/debian/patches/afetch.man.patch
===================================================================
--- trunk/packages/biosquid/trunk/debian/patches/afetch.man.patch (rev 0)
+++ trunk/packages/biosquid/trunk/debian/patches/afetch.man.patch 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,39 @@
+diff -Nur squid/Man/afetch.man squid.new/Man/afetch.man
+--- squid/Man/afetch.man 2006-07-30 18:39:11.000000000 -0300
++++ squid.new/Man/afetch.man 2006-08-05 01:47:12.000000000 -0300
+@@ -1,4 +1,4 @@
+-.TH "afetch" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual"
++.TH "afetch" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual"
+
+ .SH NAME
+ .TP
+@@ -67,15 +67,23 @@
+
+ .SH SEE ALSO
+
+-.PP
+-Master man page, with full list of and guide to the
+-individual man pages for SQUID's auxiliary programs: see
+-.B squid(1).
++.BR alistat (1),
++.BR compalign (1),
++.BR compstruct (1),
++.BR revcomp (1),
++.BR seqsplit (1),
++.BR seqstat (1),
++.BR sfetch (1),
++.BR shuffle (1),
++.BR sindex (1),
++.BR sreformat (1),
++.BR stranslate (1),
++.BR weight (1).
+
+ .SH AUTHOR
+
+- at PACKAGE@ and its documentation are @COPYRIGHT@
+- at LICENSE@
++Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
++Freely distributed under the GNU General Public License (GPL)
+ See COPYING in the source code distribution for more details, or contact me.
+
+ .nf
Added: trunk/packages/biosquid/trunk/debian/patches/alistat.man.patch
===================================================================
--- trunk/packages/biosquid/trunk/debian/patches/alistat.man.patch (rev 0)
+++ trunk/packages/biosquid/trunk/debian/patches/alistat.man.patch 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,37 @@
+diff -Nur squid/Man/alistat.man squid.new/Man/alistat.man
+--- squid/Man/alistat.man 2006-07-30 18:39:11.000000000 -0300
++++ squid.new/Man/alistat.man 2006-08-05 02:10:07.000000000 -0300
+@@ -1,4 +1,4 @@
+-.TH "alistat" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual"
++.TH "alistat" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual"
+
+ .SH NAME
+ .TP
+@@ -109,13 +109,23 @@
+
+ .SH SEE ALSO
+
+-.PP
+- at SEEALSO@
++.BR afetch (1),
++.BR compalign (1),
++.BR compstruct (1),
++.BR revcomp (1),
++.BR seqsplit (1),
++.BR seqstat (1),
++.BR sfetch (1),
++.BR shuffle (1),
++.BR sindex (1),
++.BR sreformat (1),
++.BR stranslate (1),
++.BR weight (1).
+
+ .SH AUTHOR
+
+- at PACKAGE@ and its documentation are @COPYRIGHT@
+- at LICENSE@
++Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
++Freely distributed under the GNU General Public License (GPL)
+ See COPYING in the source code distribution for more details, or contact me.
+
+ .nf
Added: trunk/packages/biosquid/trunk/debian/patches/compstruct.man.patch
===================================================================
--- trunk/packages/biosquid/trunk/debian/patches/compstruct.man.patch (rev 0)
+++ trunk/packages/biosquid/trunk/debian/patches/compstruct.man.patch 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,37 @@
+diff -Nur squid/Man/compstruct.man squid.new/Man/compstruct.man
+--- squid/Man/compstruct.man 2006-07-30 18:39:11.000000000 -0300
++++ squid.new/Man/compstruct.man 2006-08-05 02:11:13.000000000 -0300
+@@ -1,4 +1,4 @@
+-.TH "compstruct" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual"
++.TH "compstruct" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual"
+
+ .SH NAME
+ .TP
+@@ -116,13 +116,23 @@
+
+ .SH SEE ALSO
+
+-.PP
+- at SEEALSO@
++.BR afetch (1),
++.BR alistat (1),
++.BR compalign (1),
++.BR revcomp (1),
++.BR seqsplit (1),
++.BR seqstat (1),
++.BR sfetch (1),
++.BR shuffle (1),
++.BR sindex (1),
++.BR sreformat (1),
++.BR stranslate (1),
++.BR weight (1).
+
+ .SH AUTHOR
+
+- at PACKAGE@ and its documentation are @COPYRIGHT@
+- at LICENSE@
++Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
++Freely distributed under the GNU General Public License (GPL)
+ See COPYING in the source code distribution for more details, or contact me.
+
+ .nf
Added: trunk/packages/biosquid/trunk/debian/patches/seqstat.man.patch
===================================================================
--- trunk/packages/biosquid/trunk/debian/patches/seqstat.man.patch (rev 0)
+++ trunk/packages/biosquid/trunk/debian/patches/seqstat.man.patch 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,46 @@
+diff -Nur biosquid-1.9g+cvs20050121/Man/seqstat.man biosquid-1.9g+cvs20050121.new/Man/seqstat.man
+--- biosquid-1.9g+cvs20050121/Man/seqstat.man 2006-07-30 18:39:11.000000000 -0300
++++ biosquid-1.9g+cvs20050121.new/Man/seqstat.man 2008-02-21 23:03:22.000000000 -0300
+@@ -1,4 +1,4 @@
+-.TH "seqstat" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual"
++.TH "seqstat" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual"
+
+ .SH NAME
+ .TP
+@@ -16,7 +16,7 @@
+ .I seqfile
+ and shows a number of simple statistics about it.
+
+-.pp
++.PP
+ The printed statistics include the name of the format, the residue
+ type of the first sequence (protein, RNA, or DNA), the number of
+ sequences, the total number of residues, and the average and range of
+@@ -69,13 +69,23 @@
+
+ .SH SEE ALSO
+
+-.PP
+- at SEEALSO@
++.BR afetch (1),
++.BR alistat (1),
++.BR compalign (1),
++.BR compstruct (1),
++.BR revcomp (1),
++.BR seqsplit (1),
++.BR sfetch (1),
++.BR shuffle (1),
++.BR sindex (1),
++.BR sreformat (1),
++.BR stranslate (1),
++.BR weight (1).
+
+ .SH AUTHOR
+
+- at PACKAGE@ and its documentation are @COPYRIGHT@
+- at LICENSE@
++Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
++Freely distributed under the GNU General Public License (GPL)
+ See COPYING in the source code distribution for more details, or contact me.
+
+ .nf
Added: trunk/packages/biosquid/trunk/debian/patches/sfetch.man.patch
===================================================================
--- trunk/packages/biosquid/trunk/debian/patches/sfetch.man.patch (rev 0)
+++ trunk/packages/biosquid/trunk/debian/patches/sfetch.man.patch 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,46 @@
+diff -Nur biosquid-1.9g+cvs20050121/Man/sfetch.man biosquid-1.9g+cvs20050121.new/Man/sfetch.man
+--- biosquid-1.9g+cvs20050121/Man/sfetch.man 2006-07-30 18:39:11.000000000 -0300
++++ biosquid-1.9g+cvs20050121.new/Man/sfetch.man 2008-02-21 23:04:12.000000000 -0300
+@@ -1,4 +1,4 @@
+-.TH "sfetch" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual"
++.TH "sfetch" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual"
+
+ .SH NAME
+ .TP
+@@ -64,7 +64,7 @@
+ .B sindex
+ creates SSI indexes for any sequence file.
+
+-.pp
++.PP
+ .B sfetch
+ was originally named
+ .B getseq,
+@@ -191,13 +191,23 @@
+
+ .SH SEE ALSO
+
+-.PP
+- at SEEALSO@
++.BR afetch (1),
++.BR alistat (1),
++.BR compalign (1),
++.BR compstruct (1),
++.BR revcomp (1),
++.BR seqsplit (1),
++.BR seqstat (1),
++.BR shuffle (1),
++.BR sindex (1),
++.BR sreformat (1),
++.BR stranslate (1),
++.BR weight (1).
+
+ .SH AUTHOR
+
+- at PACKAGE@ and its documentation are @COPYRIGHT@
+- at LICENSE@
++Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
++Freely distributed under the GNU General Public License (GPL)
+ See COPYING in the source code distribution for more details, or contact me.
+
+ .nf
Added: trunk/packages/biosquid/trunk/debian/patches/shuffle.man.patch
===================================================================
--- trunk/packages/biosquid/trunk/debian/patches/shuffle.man.patch (rev 0)
+++ trunk/packages/biosquid/trunk/debian/patches/shuffle.man.patch 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,73 @@
+diff -Nur biosquid-1.9g+cvs20050121/Man/shuffle.man biosquid-1.9g+cvs20050121.new/Man/shuffle.man
+--- biosquid-1.9g+cvs20050121/Man/shuffle.man 2006-07-30 18:39:11.000000000 -0300
++++ biosquid-1.9g+cvs20050121.new/Man/shuffle.man 2008-02-21 23:04:46.000000000 -0300
+@@ -1,4 +1,4 @@
+-.TH "shuffle" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual"
++.TH "shuffle" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual"
+
+ .SH NAME
+ .TP
+@@ -19,7 +19,7 @@
+ are unchanged; this allows you to track down the source
+ of each randomized sequence if necessary.
+
+-.pp
++.PP
+ The default is to simply shuffle each input sequence, preserving
+ monosymbol composition exactly. To shuffle
+ each sequence while preserving both its monosymbol and disymbol
+@@ -27,7 +27,7 @@
+ .I -d
+ option.
+
+-.pp
++.PP
+ The
+ .I -0
+ and
+@@ -44,7 +44,7 @@
+ Markov properties as the input sequence (e.g.
+ the same disymbol frequencies).
+
+-.pp
++.PP
+ Note that the default and
+ .I -0,
+ or
+@@ -56,7 +56,7 @@
+ only expect to generate a sequence of similar
+ composition on average.
+
+-.pp
++.PP
+ Other shuffling algorithms are also available,
+ as documented below in the options.
+
+@@ -175,13 +175,23 @@
+
+ .SH SEE ALSO
+
+-.PP
+- at SEEALSO@
++.BR afetch (1),
++.BR alistat (1),
++.BR compalign (1),
++.BR compstruct (1),
++.BR revcomp (1),
++.BR seqsplit (1),
++.BR seqstat (1),
++.BR sfetch (1),
++.BR sindex (1),
++.BR sreformat (1),
++.BR stranslate (1),
++.BR weight (1).
+
+ .SH AUTHOR
+
+- at PACKAGE@ and its documentation are @COPYRIGHT@
+- at LICENSE@
++Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
++Freely distributed under the GNU General Public License (GPL)
+ See COPYING in the source code distribution for more details, or contact me.
+
+ .nf
Added: trunk/packages/biosquid/trunk/debian/patches/sindex.man.patch
===================================================================
--- trunk/packages/biosquid/trunk/debian/patches/sindex.man.patch (rev 0)
+++ trunk/packages/biosquid/trunk/debian/patches/sindex.man.patch 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,37 @@
+diff -Nur squid/Man/sindex.man squid.new/Man/sindex.man
+--- squid/Man/sindex.man 2006-07-30 18:39:11.000000000 -0300
++++ squid.new/Man/sindex.man 2006-08-05 02:01:43.000000000 -0300
+@@ -1,4 +1,4 @@
+-.TH "sindex" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual"
++.TH "sindex" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual"
+
+ .SH NAME
+ .TP
+@@ -83,12 +83,24 @@
+ .SH SEE ALSO
+
+ .PP
+- at SEEALSO@
++
++.BR afetch (1),
++.BR alistat (1),
++.BR compalign (1),
++.BR compstruct (1),
++.BR revcomp (1),
++.BR seqsplit (1),
++.BR seqstat (1),
++.BR sfetch (1),
++.BR shuffle (1),
++.BR sreformat (1),
++.BR stranslate (1),
++.BR weight (1).
+
+ .SH AUTHOR
+
+- at PACKAGE@ and its documentation are @COPYRIGHT@
+- at LICENSE@
++Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
++Freely distributed under the GNU General Public License (GPL)
+ See COPYING in the source code distribution for more details, or contact me.
+
+ .nf
Added: trunk/packages/biosquid/trunk/debian/patches/sreformat.man.patch
===================================================================
--- trunk/packages/biosquid/trunk/debian/patches/sreformat.man.patch (rev 0)
+++ trunk/packages/biosquid/trunk/debian/patches/sreformat.man.patch 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,55 @@
+diff -Nur biosquid-1.9g+cvs20050121/Man/sreformat.man biosquid-1.9g+cvs20050121.new/Man/sreformat.man
+--- biosquid-1.9g+cvs20050121/Man/sreformat.man 2006-07-30 18:39:11.000000000 -0300
++++ biosquid-1.9g+cvs20050121.new/Man/sreformat.man 2008-02-21 23:05:16.000000000 -0300
+@@ -1,4 +1,4 @@
+-.TH "sreformat" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual"
++.TH "sreformat" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual"
+
+ .SH NAME
+ .TP
+@@ -43,7 +43,7 @@
+ .I raw
+ (raw sequence, no other information).
+
+-.pp
++.PP
+ The available aligned output file format
+ codes include
+ .I stockholm
+@@ -59,7 +59,7 @@
+ .I selex
+ (the old SELEX/HMMER/Pfam annotated alignment format);
+
+-.pp
++.PP
+ All thee codes are interpreted case-insensitively
+ (e.g. MSF, Msf, or msf all work).
+
+@@ -231,13 +231,23 @@
+
+ .SH SEE ALSO
+
+-.PP
+- at SEEALSO@
++.BR afetch (1),
++.BR alistat (1),
++.BR compalign (1),
++.BR compstruct (1),
++.BR revcomp (1),
++.BR seqsplit (1),
++.BR seqstat (1),
++.BR sfetch (1),
++.BR shuffle (1),
++.BR sindex (1),
++.BR stranslate (1),
++.BR weight (1).
+
+ .SH AUTHOR
+
+- at PACKAGE@ and its documentation are @COPYRIGHT@
+- at LICENSE@
++Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
++Freely distributed under the GNU General Public License (GPL)
+ See COPYING in the source code distribution for more details, or contact me.
+
+ .nf
Added: trunk/packages/biosquid/trunk/debian/revcomp.1
===================================================================
--- trunk/packages/biosquid/trunk/debian/revcomp.1 (rev 0)
+++ trunk/packages/biosquid/trunk/debian/revcomp.1 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,44 @@
+.TH REVCOMP 1 "Mon, 01 Aug 2005 15:28:08 -0300"
+.SH NAME
+revcomp \- reverse complement a nucleic acid sequence
+.SH SYNOPSIS
+.B revcomp
+.RI "[-options] <seqfile>"
+.SH DESCRIPTION
+This manual page documents briefly the
+.B revcomp
+command.
+.PP
+\fBrevcomp\fP is a program that generates reverse complement of sequences.
+.SH OPTIONS
+Available options:
+.TP
+.B \-h
+Help; print version and usage info.
+.SH SEE ALSO
+.BR afetch (1),
+.BR alistat (1),
+.BR compalign (1),
+.BR compstruct (1),
+.BR seqsplit (1),
+.BR seqstat (1),
+.BR sfetch (1),
+.BR shuffle (1),
+.BR sindex (1),
+.BR sreformat (1),
+.BR stranslate (1),
+.BR weight (1).
+.br
+.SH AUTHOR
+.nf
+Sean Eddy
+HHMI/Department of Genetics
+Washington University School of Medicine
+4444 Forest Park Blvd., Box 8510
+St Louis, MO 63108 USA
+Phone: 1-314-362-7666
+FAX : 1-314-362-2157
+Email: eddy at genetics.wustl.edu
+.PP
+This manual page was written by Nelson A. de Oliveira <naoliv at gmail.com>,
+for the Debian project (but may be used by others).
Added: trunk/packages/biosquid/trunk/debian/rules
===================================================================
--- trunk/packages/biosquid/trunk/debian/rules (rev 0)
+++ trunk/packages/biosquid/trunk/debian/rules 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,14 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/rules/simple-patchsys.mk
+include /usr/share/cdbs/1/class/autotools.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+
+DEB_CONFIGURE_EXTRA_FLAGS := --enable-lfs
+DEB_MAKE_INSTALL_TARGET := install prefix=$(CURDIR)/debian/tmp
+
+makebuilddir::
+ autoconf
+
+install/biosquid::
+ mv $(CURDIR)/debian/tmp/bin/translate $(CURDIR)/debian/tmp/bin/stranslate
Property changes on: trunk/packages/biosquid/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/biosquid/trunk/debian/seqsplit.1
===================================================================
--- trunk/packages/biosquid/trunk/debian/seqsplit.1 (rev 0)
+++ trunk/packages/biosquid/trunk/debian/seqsplit.1 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,63 @@
+.TH SEQSPLIT 1 "Mon, 01 Aug 2005 15:28:08 -0300"
+.SH NAME
+seqsplit \- split seqs into chunks of defined size and overlap
+.SH SYNOPSIS
+.B seqsplit
+.RI "[-options] <seqfile>"
+.SH DESCRIPTION
+This manual page documents briefly the
+.B seqsplit
+command.
+.PP
+\fBseqsplit\fP is a program that splits sequences into smaller chunks of defined size and overlap; output a FASTA file.
+.SH OPTIONS
+.TP
+.B \-h
+Help; display usage and version.
+.TP
+.B \-o <file>
+Output the new FASTA file to <file>.
+.TP
+.B \-\-fragfile <f>
+Save one-line-per-frag coord summary file to <f>.
+.TP
+.B \-\-informat <s>
+Specify sequence file format <s>.
+.TP
+.B \-\-length <n>
+Set max length of each unique seq frag to <n>.
+.TP
+.B \-\-overlap <n>
+Set overlap length to <n> (total frag size = length+overlap).
+.TP
+.B \-\-shortnames
+Use short "frag1" names, not "<src>/<from>-<to>".
+.SH LIMITATIONS
+Still working in 32 bits -- no sequence can be more than 2 GB in size.
+.SH SEE ALSO
+.BR afetch (1),
+.BR alistat (1),
+.BR compalign (1),
+.BR compstruct (1),
+.BR revcomp (1),
+.BR seqstat (1),
+.BR sfetch (1),
+.BR shuffle (1),
+.BR sindex (1),
+.BR sreformat (1),
+.BR stranslate (1),
+.BR weight (1).
+.br
+.SH AUTHOR
+.nf
+Sean Eddy
+HHMI/Department of Genetics
+Washington University School of Medicine
+4444 Forest Park Blvd., Box 8510
+St Louis, MO 63108 USA
+Phone: 1-314-362-7666
+FAX : 1-314-362-2157
+Email: eddy at genetics.wustl.edu
+.PP
+This manual page was written by Nelson A. de Oliveira <naoliv at gmail.com>,
+for the Debian project (but may be used by others).
Added: trunk/packages/biosquid/trunk/debian/stranslate.1
===================================================================
--- trunk/packages/biosquid/trunk/debian/stranslate.1 (rev 0)
+++ trunk/packages/biosquid/trunk/debian/stranslate.1 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,73 @@
+.TH STRANSLATE 1 "Mon, 01 Aug 2005 15:28:08 -0300"
+.SH NAME
+stranslate \- translate a nucleic acid sequence to protein ORFs
+.SH SYNOPSIS
+.B stranslate
+.RI "[-options] <seqfile>"
+.SH DESCRIPTION
+This manual page documents briefly the
+.B stranslate
+command.
+.PP
+\fBstranslate\fP is a program that creates a file of all possible protein ORFs, given an input nucleic acid sequence.
+.SH OPTIONS
+Available options:
+.TP
+.B \-a
+Translate in full, with stops; no individual ORFs.
+.TP
+.B \-h
+Help; show brief usage and version info.
+.TP
+.B \-l <minlen>
+Report only ORFs greater than minlen (default 20).
+.TP
+.B \-m
+Require ORFs to start with AUG/Met.
+.TP
+.B \-o <outfile>
+Save results in output file.
+.TP
+.B \-q
+Quiet; silence banner, for piping or redirection.
+.TP
+.B \-s <stopchar>
+With \fB-a\fP, set stop character to <stopchar>.
+.TP
+.B \-\-tetrahymena
+Use the Tetrahymena/Oxytricha genetic code.
+.TP
+.B \-\-watson
+Only do the top strand (frames 0/1/2).
+.TP
+.B \-\-crick
+Only do the bottom strand (frames 3/4/5).
+.SH NOTE TO DEBIAN USERS
+The original program name is \fBtranslate\fP. It was renamed to \fBstranslate\fP to avoid conflict with another program of the same name.
+.SH SEE ALSO
+.BR afetch (1),
+.BR alistat (1),
+.BR compalign (1),
+.BR compstruct (1),
+.BR revcomp (1),
+.BR seqsplit (1),
+.BR seqstat (1),
+.BR sfetch (1),
+.BR shuffle (1),
+.BR sindex (1),
+.BR sreformat (1),
+.BR weight (1).
+.br
+.SH AUTHOR
+.nf
+Sean Eddy
+HHMI/Department of Genetics
+Washington University School of Medicine
+4444 Forest Park Blvd., Box 8510
+St Louis, MO 63108 USA
+Phone: 1-314-362-7666
+FAX : 1-314-362-2157
+Email: eddy at genetics.wustl.edu
+.PP
+This manual page was written by Nelson A. de Oliveira <naoliv at gmail.com>,
+for the Debian project (but may be used by others).
Added: trunk/packages/biosquid/trunk/debian/watch
===================================================================
--- trunk/packages/biosquid/trunk/debian/watch (rev 0)
+++ trunk/packages/biosquid/trunk/debian/watch 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,3 @@
+version=3
+opts="dversionmangle=s/\+.*//" \
+ftp://selab.janelia.org/pub/software/squid/ squid-(.*)\.tar\.gz
Added: trunk/packages/biosquid/trunk/debian/weight.1
===================================================================
--- trunk/packages/biosquid/trunk/debian/weight.1 (rev 0)
+++ trunk/packages/biosquid/trunk/debian/weight.1 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,70 @@
+.TH WEIGHT 1 "Mon, 01 Aug 2005 15:28:08 -0300"
+.SH NAME
+weight \- calculates sequence weights for an alignment
+.SH SYNOPSIS
+.B weight
+.RI "[-options] <alignment file>"
+.SH DESCRIPTION
+This manual page documents briefly the
+.B weight
+command.
+.PP
+\fBweight\fP is a program that calculates weights for a sequence alignment.
+.SH OPTIONS
+Available options:
+.TP
+.B \-b <f>
+Use BLOSUM weighting scheme at <f> fractional identity.
+.TP
+.B \-f <f>
+Filter out seqs w/ fractional ident > <x> [0-1].
+.TP
+.B \-h
+Help; print version and usage info.
+.TP
+.B \-o <file>
+Save weight-annotated alignment in <outfile>.
+.TP
+.B \-p
+Use position based weight scheme (Henikoff & Henikoff).
+.TP
+.B \-s <n>
+Sample <n> sequences at random into a new alignment.
+.TP
+.B \-v
+Use Voronoi weight scheme (Sibbald & Argos).
+.TP
+.B \-\-informat <s>
+Specify alignment file format <s>.
+.br
+Allowed formats: SELEX, MSF, Clustal, a2m, PHYLIP.
+.TP
+.B \-\-quiet
+Suppress verbose banner.
+.SH SEE ALSO
+.BR afetch (1),
+.BR alistat (1),
+.BR compalign (1),
+.BR compstruct (1),
+.BR revcomp (1),
+.BR seqsplit (1),
+.BR seqstat (1),
+.BR sfetch (1),
+.BR shuffle (1),
+.BR sindex (1),
+.BR sreformat (1),
+.BR stranslate (1),
+.br
+.SH AUTHOR
+.nf
+Sean Eddy
+HHMI/Department of Genetics
+Washington University School of Medicine
+4444 Forest Park Blvd., Box 8510
+St Louis, MO 63108 USA
+Phone: 1-314-362-7666
+FAX : 1-314-362-2157
+Email: eddy at genetics.wustl.edu
+.PP
+This manual page was written by Nelson A. de Oliveira <naoliv at gmail.com>,
+for the Debian project (but may be used by others).
Added: trunk/packages/gdpc/trunk/debian/changelog
===================================================================
--- trunk/packages/gdpc/trunk/debian/changelog (rev 0)
+++ trunk/packages/gdpc/trunk/debian/changelog 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,31 @@
+gdpc (2.2.4-3) unstable; urgency=low
+
+ * Updated gdpc homepage (Closes: #451920). Thanks Charles!
+ * Updated Standards-Version;
+ * Changed Maintainer to the Debian-Med Packaging Team;
+ * Added Vcs-* fields.
+
+ -- Nelson A. de Oliveira <naoliv at debian.org> Thu, 21 Feb 2008 23:08:51 -0300
+
+gdpc (2.2.4-2) unstable; urgency=low
+
+ * Fix FTBS with newer libgtk2.0-0 versions (Launchpad #136973)
+ Thanks to Stephan Hermann
+ - Updated patches/Makefile.diff.
+ * Updated debhelper compat level to 5;
+ * Updated my email address;
+ * Updated Standards-Version to 3.7.2;
+ * Updated deprecated ${Source-Version} to ${source:Version};
+ * Updated menu file;
+ * Updated watch file;
+ * Updated FSF address in copyright file;
+ * Added desktop file (Launchpad #36377) - Thanks to Phil Bull.
+
+ -- Nelson A. de Oliveira <naoliv at debian.org> Mon, 03 Sep 2007 12:06:20 -0300
+
+gdpc (2.2.4-1) unstable; urgency=low
+
+ * Initial Release (Closes: #306028).
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com> Sat, 23 Apr 2005 15:50:09 -0300
+
Added: trunk/packages/gdpc/trunk/debian/compat
===================================================================
--- trunk/packages/gdpc/trunk/debian/compat (rev 0)
+++ trunk/packages/gdpc/trunk/debian/compat 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1 @@
+5
Added: trunk/packages/gdpc/trunk/debian/control
===================================================================
--- trunk/packages/gdpc/trunk/debian/control (rev 0)
+++ trunk/packages/gdpc/trunk/debian/control 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,32 @@
+Source: gdpc
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Nelson A. de Oliveira <naoliv at debian.org>
+Build-Depends: cdbs, debhelper (>= 5), libgtk2.0-dev
+Standards-Version: 3.7.3
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/gdpc/trunk/
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/gdpc/trunk/
+Homepage: http://www.frantz.fi/software/gdpc.php
+
+Package: gdpc
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: gdpc-examples (>= ${source:Version}), gqview
+Description: visualiser of molecular dynamic simulations
+ gpdc is a graphical program for visualising output data from
+ molecular dynamics simulations. It reads input in the standard xyz
+ format, as well as other custom formats, and can output pictures of
+ each frame in JPG or PNG format.
+
+Package: gdpc-examples
+Architecture: all
+Recommends: gdpc (>= ${source:Version})
+Description: example files for the gdpc program
+ gpdc is a graphical program for visualising output data from
+ molecular dynamics simulations. It reads input in the standard xyz
+ format, as well as other custom formats, and can output pictures of
+ each frame in JPG or PNG format.
+ .
+ This package contains examples to be used by the gdpc program.
Added: trunk/packages/gdpc/trunk/debian/copyright
===================================================================
--- trunk/packages/gdpc/trunk/debian/copyright (rev 0)
+++ trunk/packages/gdpc/trunk/debian/copyright 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,27 @@
+This package was debianized by Nelson A. de Oliveira <naoliv at gmail.com> on
+Sat, 23 Apr 2005 15:50:09 -0300.
+
+It was downloaded from http://koti.welho.com/jfrantz/software/gdpc.html
+
+Copyright © 1999 Jonas Frantz <jonas.frantz at welho.com>
+
+License:
+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston,
+ MA 02110-1301, USA.
+
+On Debian systems, the complete text of the GNU General
+Public License can be found in `/usr/share/common-licenses/GPL'.
+
Added: trunk/packages/gdpc/trunk/debian/dirs
===================================================================
--- trunk/packages/gdpc/trunk/debian/dirs (rev 0)
+++ trunk/packages/gdpc/trunk/debian/dirs 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,2 @@
+usr/bin
+usr/share/applications
Added: trunk/packages/gdpc/trunk/debian/gdpc-examples.dirs
===================================================================
--- trunk/packages/gdpc/trunk/debian/gdpc-examples.dirs (rev 0)
+++ trunk/packages/gdpc/trunk/debian/gdpc-examples.dirs 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1 @@
+usr/share/doc/gdpc/examples/
Added: trunk/packages/gdpc/trunk/debian/gdpc-examples.install
===================================================================
--- trunk/packages/gdpc/trunk/debian/gdpc-examples.install (rev 0)
+++ trunk/packages/gdpc/trunk/debian/gdpc-examples.install 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1 @@
+*.test usr/share/doc/gdpc/examples/
Added: trunk/packages/gdpc/trunk/debian/gdpc.1
===================================================================
--- trunk/packages/gdpc/trunk/debian/gdpc.1 (rev 0)
+++ trunk/packages/gdpc/trunk/debian/gdpc.1 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,14 @@
+.TH GDPC 1 "Sun, 24 Apr 2005 02:40:13 -0300"
+.SH NAME
+gdpc \- program for visualising molecular dynamic simulations
+.SH DESCRIPTION
+This manual page documents briefly the
+.B gdpc
+command.
+.PP
+\fBgdpc\fP is a program, written in C and utilizing GTK, for visualising molecular dynamic simulations. It is a very versatile program and could easily be used for other purposes. \fBgdpc\fP reads \fIxyz\fP input and custom formats and can write out pictures of the frames.
+.SH AUTHOR
+gdpc was written by Jonas Frantz <jonas.frantz at welho.com>.
+.PP
+This manual page was written by Nelson A. de Oliveira <naoliv at gmail.com>,
+for the Debian project (but may be used by others).
Added: trunk/packages/gdpc/trunk/debian/gdpc.README.Debian
===================================================================
--- trunk/packages/gdpc/trunk/debian/gdpc.README.Debian (rev 0)
+++ trunk/packages/gdpc/trunk/debian/gdpc.README.Debian 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,37 @@
+gdpc for Debian
+---------------
+
+EXAMPLES:
+---------
+The gdpc-examples package contains 3 compressed files (liquid.test.gz,
+manytypes.test.gz and md.test.gz) located at /usr/share/doc/gdpc/examples/.
+They are included to demonstrate gdpc and to help in the process of learning
+how to use the program.
+
+KNOW CAVEATS:
+-------------
+When opening a xyz file and "Arbitrary file format" is selected on
+"Input file format" (or the opposite), gdpc will quit.
+If you run gdpc from the command prompt, it will display a message
+like this:
+
+Error in input file : 976
+
+Are you sure the input file isn't in xyz format ?
+Exiting.
+
+You must verify the type of file that you are using and that you selected
+before clicking on 'OK', or gdpc will quit if using a wrong combination
+of formats.
+
+KNOW PROBLEMS:
+--------------
+Rare: There seems to be a problem with GTK+ stability on the alpha platform,
+gdpc exits on floating exception. Seems to depend on the value of the -O
+parameter used during compilation.
+
+Weird: There seems to be some strange bug in the rotation/reset orientation
+department, sometimes reset orientation kills restart and setup button.
+May be resolved, no confirmation.
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com>, Thu, 02 Jun 2005 20:40:35 -0300
Added: trunk/packages/gdpc/trunk/debian/gdpc.desktop
===================================================================
--- trunk/packages/gdpc/trunk/debian/gdpc.desktop (rev 0)
+++ trunk/packages/gdpc/trunk/debian/gdpc.desktop 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,10 @@
+[Desktop Entry]
+Version=1.0
+Name=GDPC Molecular Dynamic Simulator
+GenericName=Molecular Dynamic Simulator
+Comment=Visualize molecular dynamic simulations
+Comment[en_GB]=Visualise molecular dynamic simulations
+Comment[pt_BR]=Visualizador de simulações moleculares dinâmicas
+Type=Application
+Exec=gdpc
+Categories=Utility;Science;Chemistry;Education;
Added: trunk/packages/gdpc/trunk/debian/gdpc.install
===================================================================
--- trunk/packages/gdpc/trunk/debian/gdpc.install (rev 0)
+++ trunk/packages/gdpc/trunk/debian/gdpc.install 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1 @@
+debian/gdpc.desktop usr/share/applications/
Added: trunk/packages/gdpc/trunk/debian/menu
===================================================================
--- trunk/packages/gdpc/trunk/debian/menu (rev 0)
+++ trunk/packages/gdpc/trunk/debian/menu 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,2 @@
+?package(gdpc):needs="X11" section="Applications/Science/Chemistry"\
+ title="gdpc" command="/usr/bin/gdpc"
Added: trunk/packages/gdpc/trunk/debian/patches/Makefile.diff
===================================================================
--- trunk/packages/gdpc/trunk/debian/patches/Makefile.diff (rev 0)
+++ trunk/packages/gdpc/trunk/debian/patches/Makefile.diff 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,21 @@
+--- old/Makefile 2005-06-01 19:30:55.000000000 -0300
++++ new/Makefile 2005-06-01 19:31:18.000000000 -0300
+@@ -1,13 +1,13 @@
+-CC = gcc -g
+-CFLAGS=-Wall `pkg-config --cflags gtk+-2.0 gthread-2.0` -DG_DISABLE_DEPRECATED -DGDK_DISABLE_DEPRECATED -DGDK_PIXBUF_DISABLE_DEPRECATED -DGTK_DISABLE_DEPRECATED
++CC = gcc
++COPTIONS=`pkg-config --cflags gtk+-2.0 gthread-2.0`
+ LIBS=`pkg-config --libs gtk+-2.0 gthread-2.0`
+-bindir ?= /usr/bin
++bindir = $(DESTDIR)/usr/bin
+
+ .c.o:
+- $(CC) -c $(CFLAGS) $(CPPFLAGS) $<
++ $(CC) -c $(COPTIONS) $(CFLAGS) $(CPPFLAGS) $<
+
+ gdpc: main.o colors.o sort.o drawatoms.o readinput.o init.o rotate.o setup.o Makefile
+- $(CC) $(CFLAGS) -o gdpc main.o colors.o drawatoms.o init.o sort.o rotate.o setup.o readinput.o $(LIBS)
++ $(CC) $(COPTIONS) $(CFLAGS) -o gdpc main.o colors.o drawatoms.o init.o sort.o rotate.o setup.o readinput.o $(LIBS)
+
+ main.o: main.c parameters.h
+
Added: trunk/packages/gdpc/trunk/debian/rules
===================================================================
--- trunk/packages/gdpc/trunk/debian/rules (rev 0)
+++ trunk/packages/gdpc/trunk/debian/rules 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,9 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/rules/simple-patchsys.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/makefile.mk
+
+DEB_DESTDIR = $(CURDIR)/debian/gdpc
+DEB_MAKE_INSTALL_TARGET := install DESTDIR=$(DEB_DESTDIR)
+DEB_INSTALL_MANPAGES_gdpc := debian/gdpc.1
Property changes on: trunk/packages/gdpc/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/gdpc/trunk/debian/watch
===================================================================
--- trunk/packages/gdpc/trunk/debian/watch (rev 0)
+++ trunk/packages/gdpc/trunk/debian/watch 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,2 @@
+version=3
+http://www.frantz.fi/index.php?page=software software/gdpc-(.*)\.tar\.gz
Added: trunk/packages/gff2aplot/trunk/debian/ali2gff.1
===================================================================
--- trunk/packages/gff2aplot/trunk/debian/ali2gff.1 (rev 0)
+++ trunk/packages/gff2aplot/trunk/debian/ali2gff.1 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,40 @@
+.TH ALI2GFF 1 "Mon, 21 Mar 2005 21:44:15 -0300"
+.SH NAME
+ali2gff \- Module to translate a MUMmer output files into gff formatted output.
+.SH SYNOPSIS
+.B ali2gff
+.RI "[-r] [-t <.|0|1|2>] [-x <name>] [-y <name>] [-H] [-f] [-h] <MUMmer_output_file>"
+.br
+.SH OPTIONS
+.TP
+.B \-h, \-\-help
+Show summary of options.
+.TP
+.B \-r
+Interchange the order of sequences (sequence 1 on y-axis, sequence 2 on x-axis).
+.TP
+.B \-t <.|0|1|2>
+Put label 'frame' in gff output.
+.TP
+.B \-x <name>
+Specify the species name for species1 (default: "Seq1").
+.TP
+.B \-y <name>
+Specify the species name for species2 (default: "Seq2").
+.TP
+.B \-i
+Ignore full sequence identities.
+.TP
+.B \-f
+Write output to file.
+.SH SEE ALSO
+.BR blat2gff (1),
+.BR gff2aplot (1),
+.BR parseblast (1),
+.BR sim2gff (1).
+.br
+.SH AUTHOR
+ali2gff was written by Steffi Gebauer-Jung.
+.PP
+This manual page was written by Nelson A. de Oliveira <naoliv at gmail.com>,
+for the Debian project (but may be used by others).
Added: trunk/packages/gff2aplot/trunk/debian/blat2gff.1
===================================================================
--- trunk/packages/gff2aplot/trunk/debian/blat2gff.1 (rev 0)
+++ trunk/packages/gff2aplot/trunk/debian/blat2gff.1 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,18 @@
+.TH BLAT2GFF 1 "Mon, 21 Mar 2005 21:44:15 -0300"
+.SH NAME
+blat2gff \- Converts BLAT output files to GFF formatted files
+.SH SYNOPSIS
+.B blat2gff
+.RI " < inputfile > outputfile"
+.br
+.SH SEE ALSO
+.BR ali2gff (1),
+.BR gff2aplot (1),
+.BR parseblast (1),
+.BR sim2gff (1).
+.br
+.SH AUTHOR
+blat2gff was written by Josep Francesc ABRIL FERRANDO <jabril at imim.es>.
+.PP
+This manual page was written by Nelson A. de Oliveira <naoliv at gmail.com>,
+for the Debian project (but may be used by others).
Added: trunk/packages/gff2aplot/trunk/debian/changelog
===================================================================
--- trunk/packages/gff2aplot/trunk/debian/changelog (rev 0)
+++ trunk/packages/gff2aplot/trunk/debian/changelog 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,42 @@
+gff2aplot (2.0-5) unstable; urgency=low
+
+ * Updated Standards-Version;
+ * Changed Maintainer to the Debian-Med Packaging Team;
+ * Added new Homepage field;
+ * Added Vcs-* fields.
+
+ -- Nelson A. de Oliveira <naoliv at debian.org> Sun, 24 Feb 2008 00:25:43 -0300
+
+gff2aplot (2.0-4) unstable; urgency=low
+
+ * Updated patches/01-makefile.diff, so ali2gff doesn't get stripped when
+ using DEB_BUILD_OPTIONS=nostrip (Closes: #436975);
+ * Updated maintainer email;
+ * Updated Standards-Version to 3.7.2;
+ * Updated compat version to 5;
+ * Updated watch file.
+
+ -- Nelson A. de Oliveira <naoliv at debian.org> Thu, 09 Aug 2007 17:16:13 -0300
+
+gff2aplot (2.0-3) unstable; urgency=low
+
+ * Not using DEB_AUTO_UPDATE_DEBIAN_CONTROL of CDBS anymore;
+ * Updated Standards-Version to 3.6.1.1 (no modifications needed).
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com> Thu, 2 Jun 2005 20:26:19 -0300
+
+gff2aplot (2.0-2) unstable; urgency=low
+
+ * debian/rules: fix DEB_AUTO_UPDATE_DEBIAN_CONTROL position;
+ * debian/control: changed ps-viewer to postscript-viewer on Suggests field;
+ * debian/control: corrected indentation of description;
+ * Included watch file.
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com> Tue, 12 Apr 2005 14:16:53 -0300
+
+gff2aplot (2.0-1) unstable; urgency=low
+
+ * Initial Release (Closes: #300828)
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com> Mon, 21 Mar 2005 20:30:45 -0300
+
Added: trunk/packages/gff2aplot/trunk/debian/compat
===================================================================
--- trunk/packages/gff2aplot/trunk/debian/compat (rev 0)
+++ trunk/packages/gff2aplot/trunk/debian/compat 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1 @@
+5
Added: trunk/packages/gff2aplot/trunk/debian/control
===================================================================
--- trunk/packages/gff2aplot/trunk/debian/control (rev 0)
+++ trunk/packages/gff2aplot/trunk/debian/control 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,53 @@
+Source: gff2aplot
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Nelson A. de Oliveira <naoliv at debian.org>
+Build-Depends: cdbs, debhelper (>= 5)
+Standards-Version: 3.7.3
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/gff2aplot/trunk/
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/gff2aplot/trunk/
+Homepage: http://genome.imim.es/software/gfftools/GFF2APLOT.html
+
+Package: gff2aplot
+Architecture: any
+Depends: ${shlibs:Depends}, ${perl:Depends}, ${misc:Depends}
+Suggests: postscript-viewer, gff2ps
+Description: pair-wise alignment-plots for genomic sequences in PostScript
+ A program to visualize the alignment of two genomic sequences together with
+ their annotations. From GFF-format input files it produces PostScript figures
+ for that alignment.
+ The following menu lists many features of gff2aplot:
+ * Comprehensive alignment plots for any GFF-feature. Attributes are defined
+ separately so you can modify only whatsoever attributes for a given file or
+ share same customization across different data-sets.
+ * All parameters are set by default within the program, but it can be also
+ fully configured via gff2ps-like flexible customization files. Program can
+ handle several of such files, summarizing all the settings before producing
+ the corresponding figure. Moreover, all customization parameters can be set
+ via command-line switches, which allows users to play with those parameters
+ before adding any to a customization file.
+ * Source order is taken from input files, if you swap file order you can
+ visualize alignment and its annotation with the new input arrangement.
+ * All alignment scores can be visualized in a PiP box below gff2aplot area,
+ using grey-color scale, user-defined color scale or score-dependent
+ gradients.
+ * Scalable fonts, which can also be chosen among the basic PostScript default
+ fonts. Feature and group labels can be rotated to improve readability in
+ both annotation axes.
+ * The program is still defined as a Unix filter so it can handle data from
+ files, redirections and pipes, writing output to standard-output and
+ warnings to standard error.
+ * gff2aplot is able to manage many physical page formats (from A0 to A10, and
+ more -see available page sizes in its manual-), including user-defined ones.
+ This allows, for instance, the generation of poster size genomic maps, or
+ the use of a continuous-paper supporting plotting device, either in portrait
+ or landscape.
+ * You can draw different alignments on same alignment plot and distinguish
+ them by using different colors for each.
+ * Shape dictionary has been expanded, so that further feature shapes are now
+ available (see manual).
+ * Annotation projections through alignment plots (so called ribbons) emulate
+ transparencies via complementary color fill patterns. This feature allows
+ to show color pseudo-blending when horizontal and vertical ribbons overlap.
Added: trunk/packages/gff2aplot/trunk/debian/copyright
===================================================================
--- trunk/packages/gff2aplot/trunk/debian/copyright (rev 0)
+++ trunk/packages/gff2aplot/trunk/debian/copyright 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,29 @@
+This package was debianized by Nelson A. de Oliveira <naoliv at gmail.com> on
+Mon, 21 Mar 2005 20:30:45 -0300.
+
+It was downloaded from http://genome.imim.es/software/gfftools/GFF2APLOT.html
+
+Copyright © 1999-2003 Josep Francesc ABRIL FERRANDO <jabril at imim.es>
+ Thomas WIEHE <rguigo at imim.es>
+ Roderic GUIGO SERRA <twiehe at zedat.fu-berlin.de>
+
+Upstream Author: Josep Francesc ABRIL FERRANDO <jabril at imim.es>
+
+License:
+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 2 of the License, or
+ (at your option) any later version..
+
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+On Debian systems, the complete text of the GNU General
+Public License can be found in `/usr/share/common-licenses/GPL'.
Added: trunk/packages/gff2aplot/trunk/debian/dirs
===================================================================
--- trunk/packages/gff2aplot/trunk/debian/dirs (rev 0)
+++ trunk/packages/gff2aplot/trunk/debian/dirs 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1 @@
+usr/bin
Added: trunk/packages/gff2aplot/trunk/debian/docs
===================================================================
--- trunk/packages/gff2aplot/trunk/debian/docs (rev 0)
+++ trunk/packages/gff2aplot/trunk/debian/docs 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,2 @@
+README
+doc/GFF2APLOT_MANUAL.ps.gz
Added: trunk/packages/gff2aplot/trunk/debian/gff2aplot.1
===================================================================
--- trunk/packages/gff2aplot/trunk/debian/gff2aplot.1 (rev 0)
+++ trunk/packages/gff2aplot/trunk/debian/gff2aplot.1 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,205 @@
+.TH GFF2APLOT 1 "Mon, 21 Mar 2005 21:44:15 -0300"
+.SH NAME
+gff2aplot \- Converting GFF files for pairwise alignments to PostScript.
+.SH SYNOPSIS
+.B gff2aplot
+.RI "[options] <GFF_files|STDIN>"
+.br
+.SH DESCRIPTION
+This manual page documents briefly the
+.B gff2aplot
+command.
+.PP
+\fBgff2aplot\fP is a program that draws color-filled alignment plots from GFF files for that alignment and two sequences annotations.
+.SH OPTIONS
+A double dash on itself "--" signals end of the options and start of file names (if present). You can use a single dash "-" as STDIN placeholder. Available options and a short description are listed here:
+.TP
+.B \-h, \-\-help
+Show summary of options.
+.TP
+.B \-\-version
+Shows current version and exits.
+.TP
+.B \-v, \-\-verbose
+Verbose mode, a full report is sent to standard error (default is set to showing only WARNINGS).
+.TP
+.B \-V, \-\-logs-filename <filename>
+Report is written to a log file.
+.TP
+.B \-q, \-\-quiet
+Quiet mode, do not show any message/warning to standard error (reporting only ERRORS).
+.TP
+.B \-p, \-\-page-size <format_name>
+Setting a page size among pre-defined ones see below for a list of available page formats).
+.TP
+.B \-\-margin-left <length>
+.TP
+.B \-\-margin-right <length>
+.TP
+.B \-\-margin-top <length>
+.TP
+.B \-\-margin-bottom <length>
+Setting each page margin to <length>. If no units are provided, points are assumed, you can use points, milimeters, centimeters or inches (pt, mm, cm or in, respectively).
+.TP
+.B \-B, \-\-background-color <color>
+Background color.
+.TP
+.B \-F, \-\-foreground-color <color>
+Foreground color.
+.TP
+.B \-T, \-\-title <string>
+Definning plot title.
+.TP
+.B \-t, \-\-subtitle <string>
+Definning plot subtitle.
+.TP
+.B \-X, \-\-x-label <string>
+Defining X-axis label.
+.TP
+.B \-Y, \-\-y-label <Y-Label>
+Defining Y-axis label.
+.TP
+.B \-L, \-\-percent-box-label <string>
+Defining percent-box label.
+.TP
+.B \-l, \-\-extra-box-label <XBox-Label>
+Definning Extra-Box Label.
+.TP
+.B \-x, \-\-x-sequence-coords <pos..pos>
+.TP
+.B \-S, \-\-start-x-sequence <pos>
+Sets X-sequence first nucleotide.
+.TP
+.B \-E, \-\-end-x-sequence <pos>
+Sets X-sequence last nucleotide.
+.TP
+.B \-y, \-\--y-sequence-coords <pos..pos>
+.TP
+.B \-s, \-\-start-y-sequence <pos>
+Sets Y-sequence first nucleotide.
+.TP
+.B \-e, \-\-end-y-sequence <pos>
+Sets Y-sequence last nucleotide.
+.TP
+.B \-\-x-sequence-zoom <pos..pos>
+.TP
+.B \-\-y-sequence-zoom <pos..pos>
+.TP
+.B \-Z, \-\-zoom [ [-S <pos>] [-E <pos>] [-s <pos>] [-e <pos>] ]
+This option zooms an area you have selected with -S,-E,-s,-e (all 4 are optional).
+.TP
+.B \-z, \-\-zoom-area [ [-S <pos>] [-E <pos>] [-s <pos>] [-e <pos>] ]
+This option marks a zoom area on your plot, but does not make a zoom.
+.TP
+.B \-A, \-\-alignment-name <SeqXName:SeqYName>
+Defining which alignment is going to be plotted if you have more than one alignment in your gff input.
+.TP
+.B \-N, \-\-x-sequence-name <SeqXName>
+Defining which sequence is going to be plotted at X-axis.
+.TP
+.B \-n, \-\-y-sequence-name <SeqYName>
+Defining which sequence is going to be plotted at Y-axis.
+.TP
+.B \-r, \-\-aplot-xy-noteq
+By default X and Y axes have same length, this option disables such behaviour, so X and Y sequence will have axes-lengths proportional to their nucleotide lengths.
+.TP
+.B \-R, \-\-xy-axes-scale <X/Y ratio>
+This option allows to set a different scale between X and Y axes lengths (by default is '1'). Below 1 values make Y larger than X, and larger than 1 result in getting X larger than Y. # Must be explained better.
+.TP
+.B \-W, \-\-aln-scale-width
+Scaling score on width for Aplot lines.
+.TP
+.B \-w, \-\-aln-scale-color
+Scaling score on color for Aplot lines.
+.TP
+.B \-K, \-\-show-ribbons <ribbon_type>
+Force Ribbons for all features on axes to be:
+(N)one, (L)ines, (R)ibbons, (B)oth.
+.TP
+.B \-G, \-\-show-grid
+Switches 'on' grid (default is 'off').
+.TP
+.B \-g, \-\-hide-grid
+Switches 'off' grid (if switched on from customization files).
+.TP
+.B \-I, \-\-show-percent-box
+Switches 'on' Percent box (default is 'off').
+.TP
+.B \-i, \-\-hide-percent-box
+Switches 'off' Percent box (if set to 'on' on custom files).
+.TP
+.B \-O, \-\-show-extra-box
+Switches 'on' Extra box (default is 'off').
+.TP
+.B \-o, \-\-hide-extra-box
+Switches 'off' Extra box (if set to 'on' on custom files).
+.TP
+.B \-D, \-\-aplot-box-color <color>
+Aplot main box background color.
+.TP
+.B \-d, \-\-percent-box-color <color>
+Percent box background color.
+.TP
+.B \-b, \-\-extra-box-color <color>
+Extra box background color.
+.TP
+.B \-\-nopswarnings
+Switch off warnings that may appear on the final PostScript figure when X sequence, Y sequence and/or alignment input data is missing.
+.TP
+.B \-a, \-\-hide-credits
+Switch off gff2aplot credits line on plot.
+.TP
+.B \-\-debug
+Reporting variable contents when testing the program. Requires that log report file option was also activated.
+.TP
+.B \-\-layout-var '<variable=value>'
+.TP
+.B \-\-sequence-var '<sequence::variable=value>'
+.TP
+.B \-\-source-var '<source::variable=value>'
+.TP
+.B \-\-strand-var '<strand::variable=value>'
+.TP
+.B \-\-group-var '<group::variable=value>'
+.TP
+.B \-\-feature-var '<feature::variable=value>'
+Loading a feature/group/strand/source/sequence/layout customization variable from command-line. You can set several variables by repeating any of these options, i.e.:
+ ... --feature-var 'cds::feature_shape=box'
+ --feature-var 'cds::feature_color=blue' ...
+.TP
+.B \-C, \-\-custom-filename <filename>
+Loading customization parameters from a given file (if default ".gff2aplotrc" exists is loaded before it).
+.TP
+Those are the colors defined in gff2aplot:
+ + Default Colors: black white.
+ + Color Palette:
+ grey pink magenta violet blue skyblue cyan seagreen
+ green limegreen yellow orange red brown
+ You can get up to nine color shades from Variable Colors with "verydeep", "deep", "verydark", "dark", "light", "verylight", "pale" and "verypale" prefixes, as example:
+ verydeepblue, deepblue, verydarkblue, darkblue, blue, lightblue, verylightblue, paleblue and verypaleblue.
+ + Dynamic colors: gradient rainbow.
+
+The following page sizes are available: from A0 to A10, from B0 to B10, 10x14, executive, folio, ledger, legal, letter, quarto, statement and tabloid.
+.SH ENVIRONMENT VARIABLES
+There are two environmental variables that can be set by users to their preferences:
+ + You can specify the path where gff2aplot can find the default files with the shell variable "GFF2APLOT_CUSTOMPATH". Default value is the path where you are running gff2aplot.
+ + You can also define the default custom filename you will like with the variable "GFF2APLOT_CUSTOMFILE", program default filename for custom file is ".gff2aplotrc".
+ + Now gff2aplot does not need to write any temporary file, so that previous versions default temporary directory path variable ("GFF2APLOT_TMP") is no longer used.
+ + Setting those vars in Bourne-shell and C-shell:
+ o Using a Bourne-Shell (e.g. bash):
+ export GFF2APLOT_CUSTOMPATH="path"
+ export GFF2APLOT_CUSTOMFILE="file_name"
+ o Using a C-Shell:
+ setenv GFF2APLOT_CUSTOMPATH "path"
+ setenv GFF2APLOT_CUSTOMFILE "file_name"
+.SH SEE ALSO
+.BR ali2gff (1),
+.BR blat2gff (1),
+.BR parseblast (1),
+.BR sim2gff (1).
+.br
+.SH AUTHOR
+gff2aplot was written by Josep Francesc ABRIL FERRANDO <jabril at imim.es>, Thomas WIEHE <twiehe at zedat.fu-berlin.de> and Roderic GUIGO SERRA <rguigo at imim.es>.
+.PP
+This manual page was written by Nelson A. de Oliveira <naoliv at gmail.com>,
+for the Debian project (but may be used by others).
Added: trunk/packages/gff2aplot/trunk/debian/parseblast.1
===================================================================
--- trunk/packages/gff2aplot/trunk/debian/parseblast.1 (rev 0)
+++ trunk/packages/gff2aplot/trunk/debian/parseblast.1 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,136 @@
+.TH PARSEBLAST 1 "Mon, 21 Mar 2005 21:44:15 -0300"
+.SH NAME
+parseblast \- Filtering High-scoring Segment Pairs (HSPs) from WU/NCBI BLAST.
+.SH SYNOPSIS
+.B parseblast
+.RI "[options] <results.from.blast>"
+.br
+.SH DESCRIPTION
+This manual page documents briefly the
+.B parseblast
+command.
+.PP
+Different output options are available, the most important here are those allowing to write HSPs in GFF format (GFFv1, GFFv2 or APLOT). Sequences can be included in the GFF records as a comment field. Furthermore, this script can output also the alignments for each HSP in ALN, MSF or tabular formats.
+
+\fBNOTE\fP - If first line from blast program output (the one containing which flavour has been run, say here BLASTN, BLASTP, BLASTX, TBLASTN or TBLASTX), is missing, the program assumes that it contains BLASTN HSP records. So that, ensure that you feed the parseblast script with a well formatted BLAST file. Sometimes there are no spaces between the HSP coords and its sequence, as it sometimes happens in Web-Blast or Paracel-Blast outputs. Now those records are processed ok and that HSP is retrieved as well as "standard" ones.
+
+\fBWARNING\fP - Frame fields from GFF records generated with parseblast contain BLAST frame (".","1","2","3") instead of the GFF standard values (".","0","1","2"). As the frame for reverse strand must be recalculated from the original sequence length, we suggest users to post-process the GFF output from this script with a suitable filter that fix the frames (in case that the program that is going to use the GFF records will not work with the original BLAST frames). We provide the command-line option "--no-frame" to set frames to "." (meaning that there is no frame).
+.SH OPTIONS
+parseblast prints output in "HSP" format by default (see below). It takes input from <STDIN> or single/multiple files, and writes its output to <STDOUT>, so user can redirect to a file but he also could use the program as a filter within a pipe.
+"-N", "-M", "-P", "-G", "-F", "-A" and "-X" options (also the long name versions for each one) are mutually exclusive, and their precedence order is shown above.
+.TP
+.B GFF OPTIONS:
+.TP
+.B \-G, \-\-gff
+Prints output in GFFv1 format.
+.TP
+.B \-F, \-\-fullgff
+Prints output in GFFv2 "alignment" format ("target").
+.TP
+.B \-A, \-\-aplot
+Prints output in pseudo-GFF APLOT "alignment" format.
+.TP
+.B \-S, \-\-subject
+Projecting GFF output by SUBJECT (default by QUERY).
+.TP
+.B \-Q, \-\-sequence
+Append query and subject sequences to GFF record.
+.TP
+.B \-b, \-\-bit-score
+Set <score> field to Bits (default Alignment Score).
+.TP
+.B \-i, \-\-identity-score
+Set <score> field to Identities (default Alignment).
+.TP
+.B \-s, \-\-full-scores
+Include all scores for each HSP in each GFF record.
+.TP
+.B \-u, \-\-no-frame
+Set all frames to "." (GFF for not available frames).
+.TP
+.B \-t, \-\-compact-tags
+Target coords+strand+frame in short form (NO GFFv2!).
+.TP
+.B ALIGNMENT OPTIONS:
+.TP
+.B \-P, \-\-pairwise
+Prints pairwise alignment for each HSP in TBL format.
+.TP
+.B \-M, \-\-msf
+Prints pairwise alignment for each HSP in MSF format.
+.TP
+.B \-N, \-\-aln
+Prints pairwise alignment for each HSP in ALN format.
+.TP
+.B \-W, \-\-show-coords
+Adds start/end positions to alignment output.
+.TP
+.B GENERAL OPTIONS:
+.TP
+.B \-X, \-\-expanded
+Expanded output (producing multiline output records).
+.TP
+.B \-c, \-\-comments
+Include parameters from blast program as comments.
+.TP
+.B \-n, \-\-no-comments
+Do not print "#" lines (raw output without comments).
+.TP
+.B \-v, \-\-verbose
+Warnings sent to <STDERR>.
+.TP
+.B \-\-version
+Prints program version and exits.
+.TP
+.B \-h, \-\-help
+Shows this help and exits.
+.SH OUTPUT FORMATS:
+ "S_" stands for "Subject_Sequence" and "Q_" for "Query_Sequence". <Program> name is taken from input blast file. <Strands> are calculated from <start> and <end> positions on original blast file. <Frame> is obtained from the blast file if is present else is set to ".". <SCORE> is set to Alignment Score by default, you can change it with "-b" and "-i".
+ If "-S" or "--subject" options are given, then QUERY fields are referred to SUBJECT and SUBJECT fields are relative to QUERY (this only available for GFF output records).
+ Dots ("...") mean that record description continues in the following line, but such record is printed as a single line record by parseblast.
+.PP
+.B [HSP] <- (This is the DEFAULT OUTPUT FORMAT)
+ <Program> <DataBase> : ...
+ ... <IdentityMatches> <Min_Length> <IdentityScore> ...
+ ... <AlignmentScore> <BitScore> <E_Value> <P_Sum> : ...
+ ... <Q_Name> <Q_Start> <Q_End> <Q_Strand> <Q_Frame> : ...
+ ... <S_Name> <S_Start> <S_End> <S_Strand> <S_Frame> : <S_FullDescription>
+.PP
+.B [GFF]
+ <Q_Name> <Program> hsp <Q_Start> <Q_End> <SCORE> <Q_Strand> <Q_Frame> <S_Name>
+.PP
+.B [FULL GFF] <- (GFF showing alignment data)
+ <Q_Name> <Program> hsp <Q_Start> <Q_End> <SCORE> <Q_Strand> <Q_Frame> ...
+ ... Target "<S_Name>" <S_Start> <S_End> ...
+ ... E_value <E_Value> Strand <S_Strand> Frame <S_Frame>
+.PP
+.B [APLOT] <- (GFF format enhanced for APLOT program)
+ <Q_Name>:<S_Name> <Program> hsp <Q_Start>:<S_Start> <Q_End>:<S_End> <SCORE> ...
+ ... <Q_Strand>:<S_Strand> <Q_Frame>:<S_Frame> <BitScore>:<HSP_Number> ...
+ ... # E_value <E_Value>
+.PP
+.B [EXPANDED]
+ MATCH(<HSP_Number>): <Q_Name> x <S_Name>
+ SCORE(<HSP_Number>): <AlignmentScore>
+ BITSC(<HSP_Number>): <BitScore>
+ EXPEC(<HSP_Number>): <E_Value> Psum(<P_Sum>)
+ IDENT(<HSP_Number>): <IdentityMatches>/<Min_Length> : <IdentityScore> %
+ T_GAP(<HSP_Number>): <TotalGaps(BothSeqs)>
+ FRAME(<HSP_Number>): <Q_Frame>/<S_Frame>
+ STRND(<HSP_Number>): <Q_Strand>/<S_Strand>
+ MXLEN(<HSP_Number>): <Max_Length>
+ QUERY(<HSP_Number>): length <Q_Length> : gaps <Q_TotalGaps> : ...
+ ... <Q_Start> <Q_End> : <Q_Strand> : <Q_Frame> : <Q_FullSequence>
+ SBJCT(<HSP_Number>): length <S_Length> : gaps <S_TotalGaps> : ...
+ ... <S_Start> <S_End> : <S_Strand> : <S_Frame> : <S_FullSequence>
+.SH SEE ALSO
+.BR ali2gff (1),
+.BR blat2gff (1),
+.BR gff2aplot (1),
+.BR sim2gff (1).
+.br
+.SH AUTHOR
+parseblast was written by Josep F. Abril <abril at imim.es>.
+.PP
+This manual page was written by Nelson A. de Oliveira <naoliv at gmail.com>,
+for the Debian project (but may be used by others).
Added: trunk/packages/gff2aplot/trunk/debian/patches/01-makefile.diff
===================================================================
--- trunk/packages/gff2aplot/trunk/debian/patches/01-makefile.diff (rev 0)
+++ trunk/packages/gff2aplot/trunk/debian/patches/01-makefile.diff 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,15 @@
+--- gff2aplot-v2_0/Makefile 2003-06-05 12:45:12.000000000 -0300
++++ gff2aplot-v2_0-new/Makefile 2005-03-22 15:22:09.000000000 -0300
+@@ -139,7 +139,11 @@
+
+ installbin : $(BINCODE)
+ @echo "### COPYING BIN FILES TO $(INSTALLDIR)...";
+- @$(CP) -p $^ $(INSTALLDIR)/;
++ /usr/bin/install -m 755 bin/ali2gff $(DESTDIR)/usr/bin
++ /usr/bin/install -m 755 bin/blat2gff.pl $(DESTDIR)/usr/bin/blat2gff
++ /usr/bin/install -m 755 bin/gff2aplot.pl $(DESTDIR)/usr/bin/gff2aplot
++ /usr/bin/install -m 755 bin/parseblast.pl $(DESTDIR)/usr/bin/parseblast
++ /usr/bin/install -m 755 bin/sim2gff.pl $(DESTDIR)/usr/bin/sim2gff
+
+ #
+ ### FINISHING CODE
Added: trunk/packages/gff2aplot/trunk/debian/patches/02-blat2gff.diff
===================================================================
--- trunk/packages/gff2aplot/trunk/debian/patches/02-blat2gff.diff (rev 0)
+++ trunk/packages/gff2aplot/trunk/debian/patches/02-blat2gff.diff 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,24 @@
+--- gff2aplot-v2_0/src/blat2gff.pl 2003-06-05 12:45:11.000000000 -0300
++++ gff2aplot-v2_0-new/src/blat2gff.pl 2005-03-21 22:46:49.000000000 -0300
+@@ -82,7 +82,7 @@
+ my @f = ();
+ next unless /^\d/o;
+ chomp;
+- @f = split /\s+/og, $_;
++ @f = split /\s+/o, $_;
+ do { # ensure that there are 21 fields
+ print STDERR "### NOT enough fields for this record:\n##### @f \n";
+ next;
+@@ -111,9 +111,9 @@
+ $gff{T_FRAME} =
+ &get_frame( $gff{T_STRAND}, $gff{T_LEN}, $gff{T_ORI}, $gff{T_END} );
+ $gff{B_NUM} = $f[ $blat{B_NUM} ];
+- @{ $gff{B_LEN} } = split /,/og, $f[ $blat{B_LEN} ];
+- @{ $gff{B_QPOS} } = split /,/og, $f[ $blat{B_QPOS} ];
+- @{ $gff{B_TPOS} } = split /,/og, $f[ $blat{B_TPOS} ];
++ @{ $gff{B_LEN} } = split /,/o, $f[ $blat{B_LEN} ];
++ @{ $gff{B_QPOS} } = split /,/o, $f[ $blat{B_QPOS} ];
++ @{ $gff{B_TPOS} } = split /,/o, $f[ $blat{B_TPOS} ];
+ printf STDOUT "# " . $GFFstring, $gff{Q_NAME}, "BLAT",
+ "$gff{Q_LEN}:$gff{T_LEN}", $gff{Q_ORI}, $gff{Q_END}, 0, $gff{Q_STRAND},
+ $gff{Q_FRAME}, "$gff{T_NAME}.$gff{GROUP}.$rec_cnt", $gff{T_ORI},
Added: trunk/packages/gff2aplot/trunk/debian/patches/03-parseblast.diff
===================================================================
--- trunk/packages/gff2aplot/trunk/debian/patches/03-parseblast.diff (rev 0)
+++ trunk/packages/gff2aplot/trunk/debian/patches/03-parseblast.diff 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,20 @@
+--- gff2aplot-v2_0/src/parseblast.pl 2005-03-22 18:27:43.000000000 -0300
++++ gff2aplot-v2_0-new/src/parseblast.pl 2005-03-22 18:39:54.000000000 -0300
+@@ -828,7 +828,7 @@
+ };
+ }; # $prt
+ #
+- ( $program, $version ) = split /\s+/og, $str, 2;
++ ( $program, $version ) = split /\s+/o, $str, 2;
+
+ # typeQ/typeS: 0 for proteins - 1 for nucleic acids.
+ # Amino Acids vs Amino Acids
+@@ -864,7 +864,7 @@
+ $prog_params = "#\n# $program $version\n#";
+ $query_name = $db_name = '';
+ };
+- ( $seqname, $descr ) = split /\s+/og, $str, 2;
++ ( $seqname, $descr ) = split /\s+/o, $str, 2;
+ $seqname =~ s/^\s*>//o;
+ $seqname =~ s/\s|:|\|/_/og;
+ $seqname .= "_" . ( $index++ );
Added: trunk/packages/gff2aplot/trunk/debian/rules
===================================================================
--- trunk/packages/gff2aplot/trunk/debian/rules (rev 0)
+++ trunk/packages/gff2aplot/trunk/debian/rules 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,14 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/rules/simple-patchsys.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/perlmodule.mk
+
+DEB_DESTDIR = $(CURDIR)/debian/gff2aplot
+DEB_MAKE_CLEAN_TARGET := clean
+DEB_MAKE_INSTALL_TARGET := install DESTDIR=$(DEB_DESTDIR) prefix=$(DEB_DESTDIR)
+DEB_INSTALL_MANPAGES_gff2aplot := debian/*.1
+DEB_INSTALL_EXAMPLES_gff2aplot := examples/*
+
+clean::
+ rm -f src/ali2gff/ali2gff bin/ali2gff
Property changes on: trunk/packages/gff2aplot/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/gff2aplot/trunk/debian/sim2gff.1
===================================================================
--- trunk/packages/gff2aplot/trunk/debian/sim2gff.1 (rev 0)
+++ trunk/packages/gff2aplot/trunk/debian/sim2gff.1 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,51 @@
+.TH SIM2GFF 1 "Mon, 21 Mar 2005 21:44:15 -0300"
+.SH NAME
+sim2gff \- Converts SIM file into GFF formatted records
+.SH SYNOPSIS
+.B sim2gff
+.RI "[-frxyHh] sim_file > gff_file"
+.br
+.SH DESCRIPTION
+This manual page documents briefly the
+.B sim2gff
+command.
+.PP
+\fBsim2gff\fP is a program written in Perl that converts SIM file into GFF formatted records (for use with gff2aplot and gff2javaplot).
+.SH OPTIONS
+.TP
+.B \-h, \-\-help
+Show summary of options.
+.TP
+.B \-f
+Output is written to a file named <sim_file>.gff.
+.TP
+.B \-r
+Interchange the order of sequences (Seq1 on y-axis, Seq2 on x-axis).
+.TP
+.B \-x <name>
+Specify the species name for species1 (default: "Seq1").
+.TP
+.B \-y <name>
+Specify the species name for species2 (default: "Seq2").
+.TP
+.B \-H
+Use the fasta file headers for species labels.
+.SH EXIT STATUS
+The following perl-like exit status are returned:
+.PP
+.B 0
+Error
+.PP
+.B 1
+Successful completion
+.SH SEE ALSO
+.BR ali2gff (1),
+.BR blat2gff (1),
+.BR gff2aplot (1),
+.BR parseblast (1).
+.br
+.SH AUTHOR
+sim2gff was written by Thomas Wiehe <twiehe at imb-jena.de>.
+.PP
+This manual page was written by Nelson A. de Oliveira <naoliv at gmail.com>,
+for the Debian project (but may be used by others).
Added: trunk/packages/gff2aplot/trunk/debian/watch
===================================================================
--- trunk/packages/gff2aplot/trunk/debian/watch (rev 0)
+++ trunk/packages/gff2aplot/trunk/debian/watch 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,2 @@
+version=3
+ftp://genome.imim.es/pub/software/gff_tools/gff2aplot/gff2aplot-v(.*)\_(.*)\.tar\.gz
Added: trunk/packages/gff2ps/trunk/debian/README.Debian
===================================================================
--- trunk/packages/gff2ps/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/gff2ps/trunk/debian/README.Debian 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,9 @@
+gff2ps for Debian
+-----------------
+
+There is an Perl implementation of gff2ps included on Bioperl package, located
+at /usr/share/doc/bioperl/examples/tools/gff2ps.pl.gz
+Note that this Perl program is very basic and limited. Also, it's not a
+ready-to-use application.
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com>, Wed, 01 Jun 2005 18:30:46 -0300
Added: trunk/packages/gff2ps/trunk/debian/changelog
===================================================================
--- trunk/packages/gff2ps/trunk/debian/changelog (rev 0)
+++ trunk/packages/gff2ps/trunk/debian/changelog 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,28 @@
+gff2ps (0.98d-3) unstable; urgency=low
+
+ * Updated Standards-Version;
+ * Changed Maintainer to the Debian-Med Packaging Team;
+ * Added new Homepage field;
+ * Added Vcs-* fields.
+
+ -- Nelson A. de Oliveira <naoliv at debian.org> Sun, 24 Feb 2008 00:18:36 -0300
+
+gff2ps (0.98d-2) unstable; urgency=low
+
+ * Updated debian/copyright file;
+ * Bumped Standards-Version to 3.7.2 (no changes needed);
+ * Moved cdbs and debhelper to Build-Depends;
+ * Using debhelper compatibility level 5;
+ * New debian/linda.override:
+ - Updated debian/rules to install the override.
+ * Removed "ghostview" from Recommends;
+ * Added a space before Homepage: on the package long description.
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com> Thu, 27 Jul 2006 02:28:37 -0300
+
+gff2ps (0.98d-1) unstable; urgency=low
+
+ * Initial Release (Closes: #310518).
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com> Tue, 22 Mar 2005 12:22:50 -0300
+
Added: trunk/packages/gff2ps/trunk/debian/compat
===================================================================
--- trunk/packages/gff2ps/trunk/debian/compat (rev 0)
+++ trunk/packages/gff2ps/trunk/debian/compat 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1 @@
+5
Added: trunk/packages/gff2ps/trunk/debian/control
===================================================================
--- trunk/packages/gff2ps/trunk/debian/control (rev 0)
+++ trunk/packages/gff2ps/trunk/debian/control 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,25 @@
+Source: gff2ps
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Nelson A. de Oliveira <naoliv at debian.org>
+Build-Depends: cdbs, debhelper (>= 5)
+Standards-Version: 3.7.3
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/gff2ps/trunk/
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/gff2ps/trunk/
+Homepage: http://genome.imim.es/software/gfftools/GFF2PS.html
+
+Package: gff2ps
+Architecture: all
+Depends: gawk, ${misc:Depends}
+Recommends: gv | postscript-viewer
+Description: produces PostScript graphical output from GFF-files
+ gff2ps is a script program developed with the aim of converting gff-formatted
+ records into high quality one-dimensional plots in PostScript. Such plots
+ maybe useful for comparing genomic structures and to visualizing outputs from
+ genome annotation programs.
+ It can be used in a very simple way, because it assumes that the GFF file
+ itself carries enough formatting information, but it also allows through a
+ number of options and/or a configuration file, for a great degree of
+ customization.
Added: trunk/packages/gff2ps/trunk/debian/copyright
===================================================================
--- trunk/packages/gff2ps/trunk/debian/copyright (rev 0)
+++ trunk/packages/gff2ps/trunk/debian/copyright 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,28 @@
+This package was debianized by Nelson A. de Oliveira <naoliv at gmail.com> on
+Tue, 22 Mar 2005 12:22:50 -0300.
+
+It was downloaded from http://genome.imim.es/software/gfftools/GFF2PS.html
+
+gff2ps
+
+ Converting GFF files to PostScript.
+
+ Copyright (C) 1999-2003 - Josep Francesc ABRIL FERRANDO
+ Roderic GUIGO SERRA
+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston,
+ MA 02110-1301, USA.
+
+On Debian systems, the GPL license can be found at /usr/share/common-licenses/
Added: trunk/packages/gff2ps/trunk/debian/dirs
===================================================================
--- trunk/packages/gff2ps/trunk/debian/dirs (rev 0)
+++ trunk/packages/gff2ps/trunk/debian/dirs 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,3 @@
+usr/bin
+usr/share/gff2ps
+usr/share/linda/overrides
Added: trunk/packages/gff2ps/trunk/debian/gff2ps.1
===================================================================
--- trunk/packages/gff2ps/trunk/debian/gff2ps.1 (rev 0)
+++ trunk/packages/gff2ps/trunk/debian/gff2ps.1 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,147 @@
+.TH GFF2PS 1 "Tue, 22 Mar 2005 12:58:35 -0300"
+.SH NAME
+gff2ps \- Produces PostScript graphical output from GFF-files.
+.SH SYNOPSIS
+.B gff2ps
+.RI "[options] -- gff_files"
+.SH DESCRIPTION
+This program draws color-filled DotPlots from files with gff-formatted data fields. The program takes as input the annotated features on a genomic sequence in GFF format, and produces a visual output in PostScript.
+.SH OPTIONS
+.TP
+.B \-h
+Show summary of options.
+.TP
+.B \-H <option>
+Shows only help for the especified option.
+.TP
+.B \-V
+Verbose mode, a full report is sent to standard error (default only sends Warnings).
+.TP
+.B \-v
+Silent mode: Disable all warnings, no messages sent to standard error.
+.TP
+.B \-d
+Write (or rewrite if exists) default customfile.
+.TP
+.B \-D <default_custom_filename>
+Create a new default customfile with the given filename.
+.TP
+.B \-C <custom_filename>
+Load given custom file and append to default custom file (.gff2psrc).
+.TP
+.B \-s <page_size>
+Useful to modify page size (default is a4).
+.TP
+.B \-p
+Switches page orientation to Portrait (default is Landscape).
+.TP
+.B \-G <color_name>
+Sets color for FOREGROUND (default is black).
+.TP
+.B \-g <color_name>
+Sets color for BACKGROUND (default is white).
+.TP
+.B \-P <#>
+Sets how many pages are needed to split your output (default is one).
+.TP
+.B \-S <#>
+Zoom first nucleotide (default is sequence origin).
+.TP
+.B \-E <#>
+Zoom last nucleotide (default is sequence length).
+.TP
+.B \-B <#>
+Sets blocks per page (default is one).
+.TP
+.B \-N <#>
+Sets nucleotides per line (default is the largest sequence position from input gff-files).
+.TP
+.B \-b
+Blocks from left to right and from top to bottom (default is top to bottom first).
+.TP
+.B \-L
+Switch off Header (Title area).
+.TP
+.B \-T <title_string>
+Defining title (default is input gff filename).
+.TP
+.B \-t <subtitle_string>
+Defining subtitle (default is none).
+.TP
+.B \-l
+Does not show page numbering.
+.TP
+.B \-O
+Does not show date.
+.TP
+.B \-o
+Does not show time.
+.TP
+.B \-M <#>
+Number of major tickmarks per line (default 10).
+.TP
+.B \-K <#>
+Major tickmarks scale in nucleotides, default is nucleotide length for lines divided by major tickmarks number (see option -T).
+.TP
+.B \-m <#>
+Number of minor tickmarks between major tickmarks (default 10).
+.TP
+.B \-k <#>
+Minor tickmarks scale in nucleotides default is major tickmarks size divided by minor tickmarks number (see option -t).
+.TP
+.B \-w, \-f
+Switch off displaying forward-strand(Watson) elements.
+.TP
+.B \-c, \-r
+Switch off displaying reverse-strand(Crick) elements.
+.TP
+.B \-i
+Switch off displaying strand-independent elements.
+.TP
+.B \-0 <color_name>
+Sets color for frame "0" (default is blue).
+.TP
+.B \-1
+Sets color for frame "1" (default is red).
+.TP
+.B \-2
+Sets color for frame "2" (default is green).
+.TP
+.B \-3
+Sets color for frame "." (default is orange).
+.TP
+.B \-n
+Switch off labels for element positions.
+.TP
+.B \-a
+Switch off CopyRight line on plot.
+.SH ENVIRONMENT VARIABLES
+There are three environmental variables that can be set by users to their pre
+ferences:
+
+ + You can specify the path where GFF2PS can find the default files with the shell variable "GFF2PS_CFDIR". Default value is path where you are running GFF2PS.
+ + You can also define the default custom filename you will like with the variable "GFF2PS_CUSTOMFILE", program default filename for custom file is ".gff2psrc".
+ + GFF2PS needs to write few temporary files in a directory with permissions for current user to read and write. Default temporary directory path is set to "/tmp/" but you can assign a different temporary directory path using the variable "GFF2PS_TMP".
+
+Setting those vars in Bourne-shell (bash):
+ export GFF2PS_CFDIR="path"
+ export GFF2PS_CUSTOMFILE="file_name"
+ export GFF2PS_TMP="path"
+
+Using a C-Shell (csh):
+ setenv GFF2PS_CFDIR "path"
+ setenv GFF2PS_CUSTOMFILE "file_name"
+ setenv GFF2PS_TMP "path"
+.SH COMMENTS
+* Colors defined are:
+ Basic Colors: black white
+ Variable Colors: grey magenta violet blue skyblue cyan seagreen green lime green yellow orange red brown
+ You can get five color shades from Variable Colors with "verydark", "dark", "light" and "verylight" prefixes. An example: verydarkseagreen darkseagreen seagreen lightseagreen verylightseagreen
+
+* Page Sizes defined are:
+ From A0 to A10, from B0 to B10, 10x14, executive, folio, ledger, legal, letter, quarto, statement and tabloid.
+.SH AUTHOR
+gff2ps was written by Josep Francesc ABRIL FERRANDO <jabril at imim.es>.
+.PP
+This manual page was written by Nelson A. de Oliveira <naoliv at gmail.com>,
+for the Debian project (but may be used by others).
Added: trunk/packages/gff2ps/trunk/debian/install
===================================================================
--- trunk/packages/gff2ps/trunk/debian/install (rev 0)
+++ trunk/packages/gff2ps/trunk/debian/install 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1 @@
+debian/wrapper/gff2ps usr/bin/
Added: trunk/packages/gff2ps/trunk/debian/linda.override
===================================================================
--- trunk/packages/gff2ps/trunk/debian/linda.override (rev 0)
+++ trunk/packages/gff2ps/trunk/debian/linda.override 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,2 @@
+Tag: exec-not-elf-or-script
+Data: /usr/share/gff2ps/gff2ps.real
Added: trunk/packages/gff2ps/trunk/debian/manpages
===================================================================
--- trunk/packages/gff2ps/trunk/debian/manpages (rev 0)
+++ trunk/packages/gff2ps/trunk/debian/manpages 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1 @@
+debian/gff2ps.1
Added: trunk/packages/gff2ps/trunk/debian/patches/01-gff2ps_v0.98d.diff
===================================================================
--- trunk/packages/gff2ps/trunk/debian/patches/01-gff2ps_v0.98d.diff (rev 0)
+++ trunk/packages/gff2ps/trunk/debian/patches/01-gff2ps_v0.98d.diff 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,11 @@
+--- gff2ps_v0.98d 2005-03-22 12:23:09.000000000 -0300
++++ gff2ps_v0.98d-new 2005-03-22 12:23:49.000000000 -0300
+@@ -39,7 +39,7 @@
+ # Only for testing (only works in bash)
+ # set -o xtrace
+
+-GAWK="/usr/local/bin/gawk";
++GAWK="/usr/bin/gawk";
+
+ ##############################################################
+ #################### PROGRAM DEFINITIONS #####################
Added: trunk/packages/gff2ps/trunk/debian/rules
===================================================================
--- trunk/packages/gff2ps/trunk/debian/rules (rev 0)
+++ trunk/packages/gff2ps/trunk/debian/rules 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,8 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/rules/simple-patchsys.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+
+install/gff2ps::
+ install -m 755 gff2ps_v0.98d debian/gff2ps/usr/share/gff2ps/gff2ps.real
+ install -m 644 debian/linda.override debian/gff2ps/usr/share/linda/overrides/gff2ps
Property changes on: trunk/packages/gff2ps/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/gff2ps/trunk/debian/watch
===================================================================
--- trunk/packages/gff2ps/trunk/debian/watch (rev 0)
+++ trunk/packages/gff2ps/trunk/debian/watch 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,3 @@
+version=3
+
+ftp://genome.imim.es/pub/gff_tools/gff2ps/gff2ps_v(.*).gz debian uupdate
Added: trunk/packages/gff2ps/trunk/debian/wrapper/gff2ps
===================================================================
--- trunk/packages/gff2ps/trunk/debian/wrapper/gff2ps (rev 0)
+++ trunk/packages/gff2ps/trunk/debian/wrapper/gff2ps 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+LC_ALL=C /usr/share/gff2ps/gff2ps.real "$@"
Added: trunk/packages/raster3d/trunk/debian/changelog
===================================================================
--- trunk/packages/raster3d/trunk/debian/changelog (rev 0)
+++ trunk/packages/raster3d/trunk/debian/changelog 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,82 @@
+raster3d (2.7d+0-2) unstable; urgency=low
+
+ * Updated Standards-Version;
+ * Changed Maintainer to the Debian-Med Packaging Team;
+ * Added new Homepage field;
+ * New patch raster3d-2.7d-gcc4-gentoo.patch from Gentoo, fixing a FTBFS bug;
+ * Added Vcs-* fields.
+
+ -- Nelson A. de Oliveira <naoliv at debian.org> Thu, 21 Feb 2008 23:24:11 -0300
+
+raster3d (2.7d+0-1) unstable; urgency=low
+
+ * Upstream author released an updated source, but with the same version
+ as before...
+ - Fixed some issues with rastep.
+ * New maintainer address;
+ * Added tags on debian/control.
+
+ -- Nelson A. de Oliveira <naoliv at debian.org> Thu, 14 Dec 2006 02:34:26 -0200
+
+raster3d (2.7d-2) unstable; urgency=low
+
+ * Rebuilt to fix dependency on uninstallable libgfortran0 (Closes: #382323);
+ * debian/control: replaced "${Source-Version}" with "${source:Version}";
+ * debian/raster3d-doc.doc-base: updated Raster3D version.
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com> Thu, 10 Aug 2006 15:41:14 -0300
+
+raster3d (2.7d-1) unstable; urgency=low
+
+ * New upstream version:
+ - Compiling with gfortran instead g77.
+ * Updated Standards-Version to 3.7.2 (no changes needed);
+ * Using debhelper compatibility version 5;
+ * Changed order of Depends (gs-gpl comes first now);
+ * Removed patches that were applied on upstream source code
+ (avs2ps.c.diff, avs2ps.l.diff, label3d.l.diff, local.c.diff,
+ normal.l.diff, r3d_objects.l.diff, r3dtops.l.diff, rastep.l.diff,
+ stereo3d.l.diff and ungz.c.diff);
+ * Removed versioned Build-Depends on cdbs and patchutils;
+ * Removed versioned Depends on imagemagick.
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com> Wed, 3 May 2006 13:31:37 -0300
+
+raster3d (2.7c-5) unstable; urgency=low
+
+ * Fix FTBFS (amd64/gcc-4.0): -malign-double makes no sense in the
+ 64bit mode (Closes: #314239).
+ Thanks to Andreas Jochens for pointing this.
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com> Thu, 16 Jun 2005 19:53:59 -0300
+
+raster3d (2.7c-4) unstable; urgency=low
+
+ * Not using DEB_AUTO_UPDATE_DEBIAN_CONTROL of CDBS anymore;
+ * Changed "gs-gpl" on Depends to "gs-afpl | gs-gpl | gs-esp".
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com> Thu, 2 Jun 2005 18:49:26 -0300
+
+raster3d (2.7c-3) unstable; urgency=low
+
+ * Wrappers for normal3d and render were not passing arguments to the real
+ programs. Corrected now.
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com> Wed, 1 Jun 2005 18:15:44 -0300
+
+raster3d (2.7c-2) unstable; urgency=low
+
+ * Clarified distribution of modified version (Closes: #308973):
+ - Updated copyright file;
+ - Included diffs between original source code and Debian's version.
+ The diffs are available at /usr/share/doc/raster3d/diffs.tar.gz
+ * Updated Standards-Version to 3.6.1.1 (no modifications needed).
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com> Mon, 16 May 2005 16:47:29 -0300
+
+raster3d (2.7c-1) unstable; urgency=low
+
+ * Initial Release (Closes: #303941).
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com> Fri, 25 Mar 2005 17:06:13 -0300
+
Added: trunk/packages/raster3d/trunk/debian/compat
===================================================================
--- trunk/packages/raster3d/trunk/debian/compat (rev 0)
+++ trunk/packages/raster3d/trunk/debian/compat 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1 @@
+5
Added: trunk/packages/raster3d/trunk/debian/control
===================================================================
--- trunk/packages/raster3d/trunk/debian/control (rev 0)
+++ trunk/packages/raster3d/trunk/debian/control 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,47 @@
+Source: raster3d
+Section: non-free/science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Nelson A. de Oliveira <naoliv at debian.org>
+Build-Depends: cdbs, debhelper (>= 5), gfortran, libtiff4-dev, libjpeg62-dev, libpng12-dev, xutils
+Standards-Version: 3.7.3
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/raster3d/trunk/
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/raster3d/trunk/
+XS-Autobuild: yes
+Homepage: http://www.bmsc.washington.edu/raster3d/raster3d.html
+
+Package: raster3d
+Architecture: any
+Depends: ${shlibs:Depends}, imagemagick, ghostscript
+Suggests: raster3d-doc (= ${source:Version})
+Description: tools for generating images of proteins or other molecules
+ Raster3D is a set of tools for generating high quality raster images of
+ proteins or other molecules. The core program renders spheres, triangles,
+ cylinders, and quadric surfaces with specular highlighting, Phong shading,
+ and shadowing. It uses an efficient software Z-buffer algorithm which is
+ independent of any graphics hardware. Ancillary programs process atomic
+ coordinates from PDB files into rendering descriptions for pictures composed
+ of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D can also be
+ used to render pictures composed in other programs such as Molscript in
+ glorious 3D with highlights, shadowing, etc. Output is to pixel image files
+ with 24 bits of color information per pixel.
+
+Package: raster3d-doc
+Section: non-free/doc
+Architecture: all
+Recommends: raster3d (= ${source:Version}), imagemagick
+Suggests: pdf-viewer, perl, www-browser
+Description: documents and example files for Raster3D
+ Raster3D is a set of tools for generating high quality raster images of
+ proteins or other molecules. The core program renders spheres, triangles,
+ cylinders, and quadric surfaces with specular highlighting, Phong shading,
+ and shadowing. It uses an efficient software Z-buffer algorithm which is
+ independent of any graphics hardware. Ancillary programs process atomic
+ coordinates from PDB files into rendering descriptions for pictures composed
+ of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D can also be
+ used to render pictures composed in other programs such as Molscript in
+ glorious 3D with highlights, shadowing, etc. Output is to pixel image files
+ with 24 bits of color information per pixel.
+ .
+ This package contains documents and example files for the raster3d package.
Added: trunk/packages/raster3d/trunk/debian/copyright
===================================================================
--- trunk/packages/raster3d/trunk/debian/copyright (rev 0)
+++ trunk/packages/raster3d/trunk/debian/copyright 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,47 @@
+This package was debianized by Nelson A. de Oliveira <naoliv at gmail.com> on
+Fri, 25 Mar 2005 17:06:13 -0300.
+
+It was downloaded from http://www.bmsc.washington.edu/raster3d/
+
+Upstream Author:
+
+Originally written by David J. Bacon and Wayne F. Anderson; extensions,
+revisions, modifications, ancillary programs by Mark Israel,
+Stephen Samuel, Michael Murphy, Albert Berghuis, and Ethan A Merritt
+<merritt at u.washington.edu> - Department of Biochemistry & Biomolecular
+Structure Center - University of Washington, Seattle
+
+Copyright 1996-2006 © Ethan Merritt and others.
+
+ Copyright to the Raster3D code is held by Ethan Merritt and
+ other contributors. The code may be used or modified without
+ restriction. Modified versions may only be redistributed with
+ prior permission and must be accompanied by source code patches
+ against a previous official release of the Raster3D source code.
+
+Permission from Ethan, to distribute Raster3D on Debian:
+
+It is fine to use Raster3D for commercial purposes;
+in fact you can see from the covers of many scientific journals that it is
+used for this by many publishers. Raster3D may not be sold, however.
+
+As I told you, I have explicitly given Debian permission to include
+Raster3D in the past, but it never seems to emerge from the other
+end of the process.
+
+CITING THE PROGRAM
+If you use the package to prepare figures for publication, please give
+proper credit to the authors; the proper citation for the most recent
+version of the package is Merritt & Bacon (1997) as given below.
+
+REFERENCES
+Bacon, D.J., & Anderson, W.F. (1988) ``A Fast Algorithm for
+Rendering Space-Filling Molecule Pictures''. (abstract of paper
+presented at the Seventh Annual Meeting of the Molecular Graphics
+Society). J. Molec. Graphics 6, 219-220.
+Kraulis, P.J. (1991) ``MOLSCRIPT: a program to produce both detailed
+and schematic plots of protein structures''. J. Appl. Cryst. 24, 946-950.
+Merritt, E.A. & Murphy, M.E.P. (1994) ``Raster3D Version 2.0 - A Program
+for Photorealistic Molecular Graphics''. Acta Cryst. D50, 869-873.
+Merritt, E.A. & Bacon, D.J. (1997) ``Raster3D Photorealistic Molecular
+Graphics''. Methods in Enzymology 277, 505-524.
Added: trunk/packages/raster3d/trunk/debian/install
===================================================================
--- trunk/packages/raster3d/trunk/debian/install (rev 0)
+++ trunk/packages/raster3d/trunk/debian/install 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,13 @@
+debian/tmp/bin/avs2ps usr/bin/
+debian/tmp/bin/balls usr/bin/
+debian/tmp/bin/label3d usr/bin/
+debian/tmp/bin/rastep usr/bin/
+debian/tmp/bin/ribbon usr/bin/
+debian/tmp/bin/rings3d usr/bin/
+debian/tmp/bin/rods usr/bin/
+debian/tmp/bin/stereo3d usr/bin/
+debian/tmp/bin/*.real usr/lib/raster3d/
+debian/tmp/share/man/ usr/share/
+debian/wrappers/* usr/bin/
+materials/ usr/share/raster3d/
+debian/diffs.tar usr/share/doc/raster3d/
Added: trunk/packages/raster3d/trunk/debian/patches/BUGS.diff
===================================================================
--- trunk/packages/raster3d/trunk/debian/patches/BUGS.diff (rev 0)
+++ trunk/packages/raster3d/trunk/debian/patches/BUGS.diff 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,51 @@
+diff -Nur raster3d-2.7d/BUGS raster3d-2.7d.new/BUGS
+--- raster3d-2.7d/BUGS 2006-04-11 15:52:29.000000000 -0300
++++ raster3d-2.7d.new/BUGS 2006-05-03 18:15:37.000000000 -0300
+@@ -1,11 +1,3 @@
+-All platforms
+-=============
+-
+- ==> ImageMagick keeps on changing their option syntax and delegates
+- file format. You may have to tweak the calls to ImageMagick
+- utilities in the stereo3d and label3d scripts to match your local
+- version of ImageMagick.
+-
+ ==> Stereo pairs can be generated by using either a shear operation or
+ by using an angular offset. Both have problems. The shear distorts
+ bounding surfaces. The angular offset displaces specular highlights
+@@ -28,35 +20,3 @@
+ - Labels with TeX-like escape sequences are always treated as Left-Align.
+ - Angstrom symbol only loaded into Times/Helvetica fonts.
+ - ribbon coloring scheme 6 doesn't work
+-
+-SGI
+-===
+- - In general the JPEG and PNG libraries supplied with Irix are bad,
+- and should be rebuilt from current source
+- - Some versions of Irix contain a header file jpeglib.h that is not
+- compatible with the actual libjpeg in the same distribution
+- - The PNG library and header files are from an ancient beta-test version.
+- You must choose between disabling PNG support in Makefile.template or
+- installing a newer version of libpng on your machine
+-
+-AIX
+-===
+- File indirection in render doesn't work, because opening Fortran
+- LUN 6 clobbers C I/O in local.c
+- Work-around :
+- Patch file render_patch.aix modifies render to use
+- LUNs 5,4,3,2,1 for file indirection rather than 6,7,...
+- dispose='delete' not permitted in open statement
+- Work-around :
+- None; temp files accumulate until deleted
+-
+-linux (g77 and gfortran compilers)
+-====================
+-
+- The g77 and gfortran compilers do not support file open options
+- CARRIAGECONTROL='LIST' or DISPOSE='DELETE'.
+- Work-around :
+- 'make linux' deletes these specifications from the source
+- files; unfortunately, this means that temporary files do not
+- automatically get deleted from the system temp directory.
+-
Added: trunk/packages/raster3d/trunk/debian/patches/Makefile.diff
===================================================================
--- trunk/packages/raster3d/trunk/debian/patches/Makefile.diff (rev 0)
+++ trunk/packages/raster3d/trunk/debian/patches/Makefile.diff 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,32 @@
+diff -Nur raster3d-2.7d/Makefile raster3d-2.7d.new/Makefile
+--- raster3d-2.7d/Makefile 2006-04-12 15:46:10.000000000 -0300
++++ raster3d-2.7d.new/Makefile 2006-05-03 18:20:33.000000000 -0300
+@@ -61,9 +61,9 @@
+ @cp Makefile.template Makefile.incl
+ @echo OS = linux >> Makefile.incl
+ @echo CC = gcc >> Makefile.incl
+- @echo CFLAGS = -g -w -Dgfortran >> Makefile.incl
++ @echo CFLAGS = -g -O2 -Wall -Dgfortran >> Makefile.incl
+ @echo FC = gfortran >> Makefile.incl
+- @echo FFLAGS = -g -w -O -ffixed-line-length-132 >> Makefile.incl
++ @echo FFLAGS = -g -Wall -O2 -ffixed-line-length-132 >> Makefile.incl
+ @echo RM = /bin/rm -f >> Makefile.incl
+ @echo OSDEFS = -DLINUX -DNETWORKBYTEORDER >> Makefile.incl
+ @echo include Makefile.package >> Makefile.incl
+@@ -222,12 +222,14 @@
+ install: all
+ if [ ! -e $(prefix) ] ; then mkdirhier $(prefix) ; fi
+ if [ ! -e $(bindir) ] ; then mkdirhier $(bindir) ; fi
+- chmod 755 $(PROGS); cp $(PROGS) $(bindir)
++ chmod 755 $(PROGS);
++ for i in normal3d render; do cp $$i $(bindir)/$$i.real; done
++ cp avs2ps balls label3d rastep ribbon rings3d rods stereo3d $(bindir)
+ chmod 755 $(SCRIPTS); cp $(SCRIPTS) $(bindir)
+ if [ ! -e $(datadir) ] ; then mkdirhier $(datadir) ; fi
+ cp materials/* $(datadir)
+ if [ ! -e $(mandir) ] ; then mkdirhier $(mandir) ; fi
+- cp doc/*.l $(mandir)
++ for i in doc/*.l; do j=$${i/doc/}; cp $$i $(mandir)/$${j/.l/.1}; done
+ if [ ! -e $(htmldir) ] ; then mkdirhier $(htmldir) ; fi
+ cp html/* $(htmldir)
+ if [ ! -e $(examdir) ] ; then mkdirhier $(examdir) ; fi
Added: trunk/packages/raster3d/trunk/debian/patches/Makefile.template.diff
===================================================================
--- trunk/packages/raster3d/trunk/debian/patches/Makefile.template.diff (rev 0)
+++ trunk/packages/raster3d/trunk/debian/patches/Makefile.template.diff 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,24 @@
+--- raster3d-2.7c.orig/Makefile.template 2003-10-20 20:50:11.000000000 -0200
++++ raster3d-2.7c.new/Makefile.template 2005-04-01 17:39:19.000000000 -0300
+@@ -8,15 +8,15 @@
+ #
+ # Where to install the program, data files, and manuals
+ #
+-prefix = /usr/local
++prefix = /usr
+ bindir = $(prefix)/bin
+-datadir = $(prefix)/share/Raster3D/materials
+-mandir = $(prefix)/man/manl
+-htmldir = $(prefix)/share/Raster3D/html
+-examdir = $(prefix)/share/Raster3D/examples
++datadir = $(prefix)/share/raster3d/materials
++mandir = $(prefix)/share/man/man1
++htmldir = $(prefix)/share/raster3d/html
++examdir = $(prefix)/share/raster3d/examples
+
+ INCDIRS = -I/usr/include -I/usr/local/include
+-LIBDIRS = -L/usr/local/lib
++LIBDIRS = -L/usr/lib
+
+ #
+ # TIFF support (enabled by default)
Added: trunk/packages/raster3d/trunk/debian/patches/example1.script.diff
===================================================================
--- trunk/packages/raster3d/trunk/debian/patches/example1.script.diff (rev 0)
+++ trunk/packages/raster3d/trunk/debian/patches/example1.script.diff 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,15 @@
+--- raster3d-2.7c.orig/examples/example1.script
++++ raster3d-2.7c/examples/example1.script
+@@ -1,4 +1,4 @@
+-#!/bin/csh
++#!/bin/bash
+ # E A Merritt January 2003
+ # Illustration of
+ # material properties
+@@ -6,5 +6,5 @@
+ # R3D_LIB environmental variable
+ # gamma correction applied while rendering
+ #
+-setenv R3D_LIB ../materials
++export R3D_LIB="../materials"
+ render -gamma 1.1 -png < example1.r3d | display png:-
Added: trunk/packages/raster3d/trunk/debian/patches/example2.script.diff
===================================================================
--- trunk/packages/raster3d/trunk/debian/patches/example2.script.diff (rev 0)
+++ trunk/packages/raster3d/trunk/debian/patches/example2.script.diff 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,18 @@
+--- raster3d-2.7c.orig/examples/example2.script
++++ raster3d-2.7c/examples/example2.script
+@@ -1,11 +1,11 @@
+-#!/bin/csh
++#!/bin/bash
+ # E A Merritt March 1993
+ # Illustration of composed figure using Raster3D
+ # (assumes ImageMagick installed, if not then don't pipe output from render)
+ #
+-setenv TMPFILE `mktemp /tmp/ex2.XXXXXX` || exit 1
+-setenv TMPBALLS `mktemp /tmp/ex2.XXXXXX` || exit 1
+-setenv TMPSUGAR `mktemp /tmp/ex2.XXXXXX` || exit 1
++export TMPFILE=`mktemp /tmp/ex2.XXXXXX` || exit 1
++export TMPBALLS=`mktemp /tmp/ex2.XXXXXX` || exit 1
++export TMPSUGAR=`mktemp /tmp/ex2.XXXXXX` || exit 1
+ #
+ # figure consists of E. coli enterotoxin (protein as spheres)
+ # binding to GM1 pentasaccharide (sugars represented as rods)
Added: trunk/packages/raster3d/trunk/debian/patches/example2.sgi.diff
===================================================================
--- trunk/packages/raster3d/trunk/debian/patches/example2.sgi.diff (rev 0)
+++ trunk/packages/raster3d/trunk/debian/patches/example2.sgi.diff 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,8 @@
+--- raster3d-2.7c.orig/examples/example2.sgi
++++ raster3d-2.7c/examples/example2.sgi
+@@ -1,4 +1,4 @@
+-#!/bin/csh
++#!/bin/bash
+ # E A Merritt March 1993
+ # Illustration of composed figure using Raster3D
+ # (assumes libimage support from 4DGifts distribution kit on SGI)
Added: trunk/packages/raster3d/trunk/debian/patches/example3.script.diff
===================================================================
--- trunk/packages/raster3d/trunk/debian/patches/example3.script.diff (rev 0)
+++ trunk/packages/raster3d/trunk/debian/patches/example3.script.diff 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,8 @@
+--- raster3d-2.7c.orig/examples/example3.script
++++ raster3d-2.7c/examples/example3.script
+@@ -1,4 +1,4 @@
+-#!/bin/csh
++#!/bin/bash
+ # E A Merritt March 1993
+ # Illustration of simple figure using Raster3D
+ # Assumes ImageMagick installed, if you are using the SGI libimage
Added: trunk/packages/raster3d/trunk/debian/patches/example4.script.diff
===================================================================
--- trunk/packages/raster3d/trunk/debian/patches/example4.script.diff (rev 0)
+++ trunk/packages/raster3d/trunk/debian/patches/example4.script.diff 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,8 @@
+--- raster3d-2.7c.orig/examples/example4.script
++++ raster3d-2.7c/examples/example4.script
+@@ -1,4 +1,4 @@
+-#!/bin/csh
++#!/bin/bash
+ # E A Merritt April 2002
+ # Illustration of combined Molscript/Raster3D application
+ #
Added: trunk/packages/raster3d/trunk/debian/patches/example5.script.diff
===================================================================
--- trunk/packages/raster3d/trunk/debian/patches/example5.script.diff (rev 0)
+++ trunk/packages/raster3d/trunk/debian/patches/example5.script.diff 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,8 @@
+--- raster3d-2.7c.orig/examples/example5.script
++++ raster3d-2.7c/examples/example5.script
+@@ -1,4 +1,4 @@
+-#!/bin/csh
++#!/bin/bash
+ # E A Merritt November 2000
+ # Illustration of complex figure created by merging files from
+ # Raster3D, Molscript, and GRASP.
Added: trunk/packages/raster3d/trunk/debian/patches/example6.script.diff
===================================================================
--- trunk/packages/raster3d/trunk/debian/patches/example6.script.diff (rev 0)
+++ trunk/packages/raster3d/trunk/debian/patches/example6.script.diff 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,8 @@
+--- raster3d-2.7c.orig/examples/example6.script
++++ raster3d-2.7c/examples/example6.script
+@@ -1,4 +1,4 @@
+-#!/bin/csh
++#!/bin/bash
+ # E A Merritt November 1999
+ # Illustration of V2.5 command line options
+ # Assumes ImageMagick installed
Added: trunk/packages/raster3d/trunk/debian/patches/example7.script.diff
===================================================================
--- trunk/packages/raster3d/trunk/debian/patches/example7.script.diff (rev 0)
+++ trunk/packages/raster3d/trunk/debian/patches/example7.script.diff 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,8 @@
+--- raster3d-2.7c.orig/examples/example7.script
++++ raster3d-2.7c/examples/example7.script
+@@ -1,4 +1,4 @@
+-#!/bin/csh
++#!/bin/bash
+ #
+ # Example 7
+ #
Added: trunk/packages/raster3d/trunk/debian/patches/example8.script.diff
===================================================================
--- trunk/packages/raster3d/trunk/debian/patches/example8.script.diff (rev 0)
+++ trunk/packages/raster3d/trunk/debian/patches/example8.script.diff 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,19 @@
+--- raster3d-2.7c.orig/examples/example8.script
++++ raster3d-2.7c/examples/example8.script
+@@ -1,9 +1,14 @@
+-#!/bin/csh
++#!/bin/bash
+ #
+ # Demonstrate stereo3d script by making stereo pair of
+ # view down pore of LT B-pentamer
+ #
+-if (! $?TMPDIR) setenv TMPDIR /tmp ; endif
++if [ "$TMPDIR" ]; then
++ tmp=$TMPDIR
++else
++ tmp=/tmp
++fi
++export TMPDIR=$tmp
+ #
+ # First we make a VDW model of the B-pentamer itself
+ #
Added: trunk/packages/raster3d/trunk/debian/patches/example9.script.diff
===================================================================
--- trunk/packages/raster3d/trunk/debian/patches/example9.script.diff (rev 0)
+++ trunk/packages/raster3d/trunk/debian/patches/example9.script.diff 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,8 @@
+--- raster3d-2.7c.orig/examples/example9.script
++++ raster3d-2.7c/examples/example9.script
+@@ -1,4 +1,4 @@
+-#!/bin/csh
++#!/bin/bash
+ #
+ # Thermal ellipsoid representations
+ # GM1-pentasaccharide from a complex with the cholera toxin B-pentamer
Added: trunk/packages/raster3d/trunk/debian/patches/msms_example.script.diff
===================================================================
--- trunk/packages/raster3d/trunk/debian/patches/msms_example.script.diff (rev 0)
+++ trunk/packages/raster3d/trunk/debian/patches/msms_example.script.diff 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,8 @@
+--- raster3d-2.7c.orig/examples/msms/msms_example.script
++++ raster3d-2.7c/examples/msms/msms_example.script
+@@ -1,4 +1,4 @@
+-#!/bin/csh
++#!/bin/bash
+ #
+ # Calculate molecular surface of a galactose molecule using MSMS
+ #
Added: trunk/packages/raster3d/trunk/debian/patches/r3d_objects.man.diff
===================================================================
--- trunk/packages/raster3d/trunk/debian/patches/r3d_objects.man.diff (rev 0)
+++ trunk/packages/raster3d/trunk/debian/patches/r3d_objects.man.diff 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,17 @@
+diff -Nur raster3d-2.7d+0/doc/r3d_objects.l raster3d-2.7d+0.new/doc/r3d_objects.l
+--- raster3d-2.7d+0/doc/r3d_objects.l 2006-04-11 16:34:54.000000000 -0300
++++ raster3d-2.7d+0.new/doc/r3d_objects.l 2008-02-22 00:10:25.000000000 -0300
+@@ -1,9 +1,11 @@
+-.l
++.ad l
+ .nh
+ .TH R3D_OBJECTS 1 " 8 May 1999" "Raster3D"
+ .SH NAME
+-Object types used by the Raster3D package
+
++rd3_objects - object types used by the Raster3D package
++
++.SH DESCRIPTION
+ These are the object descriptor types, and the required
+ parameters, recognized by the \fBrender\fP program and
+ other components of the Raster3D package.
Added: trunk/packages/raster3d/trunk/debian/patches/raster3d-2.7d-gcc4-gentoo.patch
===================================================================
--- trunk/packages/raster3d/trunk/debian/patches/raster3d-2.7d-gcc4-gentoo.patch (rev 0)
+++ trunk/packages/raster3d/trunk/debian/patches/raster3d-2.7d-gcc4-gentoo.patch 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,38 @@
+diff -Naur Raster3D_2.7d/normal3d.f Raster3D_2.7d.new/normal3d.f
+--- Raster3D_2.7d/normal3d.f 2003-10-20 18:50:11.000000000 -0400
++++ Raster3D_2.7d.new/normal3d.f 2007-09-08 10:12:49.000000000 -0400
+@@ -443,7 +443,8 @@
+ READ (INPUT,'(A)',ERR=101) TITLE
+ IF (TITLE(1:1).EQ.'#') GOTO 100
+ GOTO 102
+- 101 WRITE (NOISE,'(A,A)') ' >> Cannot open or read file ',TITLE(2:132)
++ 101 WRITE (NOISE,'(A,A)') ' >> Cannot open or read file ',
++ *TITLE(2:132)
+ CALL EXIT(-1)
+ 102 CONTINUE
+ ENDIF
+diff -Naur Raster3D_2.7d/parse.f Raster3D_2.7d.new/parse.f
+--- Raster3D_2.7d/parse.f 2006-04-11 14:33:48.000000000 -0400
++++ Raster3D_2.7d.new/parse.f 2007-09-08 10:25:24.000000000 -0400
+@@ -4,7 +4,8 @@
+ COMMON /OPTIONS/ FONTSCALE, GAMMA, ZOOM, NSCHEME, SHADOWFLAG, XBG,
+ & NAX, NAY, OTMODE, QUALITY, INVERT, LFLAG
+ REAL FONTSCALE, GAMMA, ZOOM
+- INTEGER NSCHEME, SHADOWFLAG, XBG
++ INTEGER NSCHEME, SHADOWFLAG
++ INTEGER*8 XBG
+ INTEGER*2 NAX, NAY, OTMODE, QUALITY
+ LOGICAL*2 INVERT, LFLAG
+ c
+diff -Naur Raster3D_2.7d/render.f Raster3D_2.7d.new/render.f
+--- Raster3D_2.7d/render.f 2006-04-11 17:13:04.000000000 -0400
++++ Raster3D_2.7d.new/render.f 2007-09-08 10:15:17.000000000 -0400
+@@ -3685,7 +3685,7 @@
+ FRAC = DETAIL(K+8)
+ INEXT = INDTOP + 1
+ IF (TYPE(INEXT).EQ.VERTEXRGB) INEXT = INEXT + 1
+- CALL ASSERT(TYPE(INEXT).EQ.VERTRANSP,'lost vertex transp')
++ CALL ASSERT(TYPE(INEXT).EQ.VERTRANSP,'lost vertex transp')
+ K = LIST(INEXT)
+ CLRITY = FRAC*DETAIL(K+1) + (1.-FRAC)*DETAIL(K+2)
+ ELSE IF (TYPE(INDTOP).EQ.TRIANG) THEN
Added: trunk/packages/raster3d/trunk/debian/patches/raster3d.man.diff
===================================================================
--- trunk/packages/raster3d/trunk/debian/patches/raster3d.man.diff (rev 0)
+++ trunk/packages/raster3d/trunk/debian/patches/raster3d.man.diff 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,13 @@
+diff -Nur raster3d-2.7d+0/doc/raster3d.l raster3d-2.7d+0.new/doc/raster3d.l
+--- raster3d-2.7d+0/doc/raster3d.l 2006-04-11 16:36:24.000000000 -0300
++++ raster3d-2.7d+0.new/doc/raster3d.l 2008-02-22 00:12:57.000000000 -0300
+@@ -2,8 +2,7 @@
+ .nh
+ .TH Raster3D 1 "28 August 2001" "Raster3D V2.6"
+ .SH NAME
+-.PP
+-Raster3D molecular graphics package
++Raster3D - molecular graphics package
+ .SH SYNOPSIS
+ .PP
+ The \fIRaster3D\fP molecular graphics package consists of a core
Added: trunk/packages/raster3d/trunk/debian/patches/render.man.diff
===================================================================
--- trunk/packages/raster3d/trunk/debian/patches/render.man.diff (rev 0)
+++ trunk/packages/raster3d/trunk/debian/patches/render.man.diff 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,9 @@
+diff -Nur raster3d-2.7d+0/doc/render.l raster3d-2.7d+0.new/doc/render.l
+--- raster3d-2.7d+0/doc/render.l 2006-04-11 16:36:34.000000000 -0300
++++ raster3d-2.7d+0.new/doc/render.l 2008-02-22 00:07:26.000000000 -0300
+@@ -1,4 +1,4 @@
+-.l
++.ad l
+ .nh
+ .TH RENDER 1 "19 May 2003" "Raster3D"
+ .SH NAME
Added: trunk/packages/raster3d/trunk/debian/patches/rods.man.diff
===================================================================
--- trunk/packages/raster3d/trunk/debian/patches/rods.man.diff (rev 0)
+++ trunk/packages/raster3d/trunk/debian/patches/rods.man.diff 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,14 @@
+diff -Nur raster3d-2.7d+0/doc/rods.l raster3d-2.7d+0.new/doc/rods.l
+--- raster3d-2.7d+0/doc/rods.l 2006-04-11 16:36:44.000000000 -0300
++++ raster3d-2.7d+0.new/doc/rods.l 2008-02-22 00:08:48.000000000 -0300
+@@ -5,8 +5,8 @@
+
+ rods - Raster3D preprocessor for ball-and-stick models
+ .SH SYNOPSIS
+-
+-.HB rods [\fI-h\fP] [\fI-b\fP] [\fI-radius R\fP] \fI[-Bcolor Bmin Bmax\fP]
++.PP
++.B rods [\fI-h\fP] [\fI-b\fP] [\fI-radius R\fP] \fI[-Bcolor Bmin Bmax\fP]
+ .PP
+ \fIRods\fP reads a file describing atom colours and/or a
+ PDB coordinate file and produces a file containing Raster3D descriptor
Added: trunk/packages/raster3d/trunk/debian/raster3d-doc.README.Debian
===================================================================
--- trunk/packages/raster3d/trunk/debian/raster3d-doc.README.Debian (rev 0)
+++ trunk/packages/raster3d/trunk/debian/raster3d-doc.README.Debian 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,8 @@
+raster3d-doc for Debian
+--------------------
+
+Note that some examples included on raster3d-doc needs raster3d and
+imagemagick packages installed to run properly. If you want to get full
+functionality of the example scripts, you need to install them.
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com>, Sun, 10 Apr 2005 00:17:27 -0300
Added: trunk/packages/raster3d/trunk/debian/raster3d-doc.doc-base
===================================================================
--- trunk/packages/raster3d/trunk/debian/raster3d-doc.doc-base (rev 0)
+++ trunk/packages/raster3d/trunk/debian/raster3d-doc.doc-base 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,16 @@
+Document: raster3d
+Title: Raster3D 2.7d Manual
+Author: Ethan. A Merritt
+Abstract: The Raster3D molecular graphics package consists of a core program
+ (render) and a number of ancillary programs that read atomic coordinates from
+ PDB (Protein Data Bank) files to produce scene descriptions for input to
+ render. Raster3D can also render images composed using other programs such
+ as Molscript and XtalView.
+Section: Apps/Science
+
+Format: PDF
+Files: /usr/share/doc/raster3d/R3D_manual.pdf.gz
+
+Format: HTML
+Index: /usr/share/doc/raster3d/html/index.html
+Files: /usr/share/doc/raster3d/html/*.html
Added: trunk/packages/raster3d/trunk/debian/raster3d-doc.install
===================================================================
--- trunk/packages/raster3d/trunk/debian/raster3d-doc.install (rev 0)
+++ trunk/packages/raster3d/trunk/debian/raster3d-doc.install 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,3 @@
+doc/R3D_manual.pdf usr/share/doc/raster3d/
+debian/tmp/share/raster3d/examples/ usr/share/doc/raster3d/
+debian/tmp/share/raster3d/html/ usr/share/doc/raster3d/
Added: trunk/packages/raster3d/trunk/debian/raster3d-doc.links
===================================================================
--- trunk/packages/raster3d/trunk/debian/raster3d-doc.links (rev 0)
+++ trunk/packages/raster3d/trunk/debian/raster3d-doc.links 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1 @@
+usr/share/doc/raster3d/html/raster3d.html usr/share/doc/raster3d/html/index.html
Added: trunk/packages/raster3d/trunk/debian/raster3d.README.Debian
===================================================================
--- trunk/packages/raster3d/trunk/debian/raster3d.README.Debian (rev 0)
+++ trunk/packages/raster3d/trunk/debian/raster3d.README.Debian 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,15 @@
+raster3d for Debian
+--------------------
+
+The raster3d-doc package might be important for new users or people
+wanting to learn more about Raster3D. Besides manuals in HTML and
+PDF formats (complementing the already included man pages on raster3d
+package), raster3d-doc also contains example files (PDBs, images and
+scripts) showing Raster3D's capabilities.
+
+/usr/share/doc/raster3d/diffs.tar.gz
+This file has the diffs between original source code of Raster3D and
+Debian's version. Upstream author allowed to distribute modified
+versions of his program if the differences were included.
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com>, Sun, 10 Apr 2005 00:17:27 -0300
Added: trunk/packages/raster3d/trunk/debian/raster3d.docs
===================================================================
--- trunk/packages/raster3d/trunk/debian/raster3d.docs (rev 0)
+++ trunk/packages/raster3d/trunk/debian/raster3d.docs 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1 @@
+BUGS
Added: trunk/packages/raster3d/trunk/debian/raster3d.manpages
===================================================================
--- trunk/packages/raster3d/trunk/debian/raster3d.manpages (rev 0)
+++ trunk/packages/raster3d/trunk/debian/raster3d.manpages 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1 @@
+debian/rings3d.1
Added: trunk/packages/raster3d/trunk/debian/rings3d.1
===================================================================
--- trunk/packages/raster3d/trunk/debian/rings3d.1 (rev 0)
+++ trunk/packages/raster3d/trunk/debian/rings3d.1 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,78 @@
+.ad l
+.nh
+.TH RINGS3D 1 "" "Raster3D"
+.SH NAME
+
+rigns3d - produces a file of ring-filling triangles from a PDB file
+
+.SH SYNOPSIS
+
+rings3d [-bases] [-protein] [-sugars] < infile.pdb > outfile.r3d
+
+.PP
+\fIrings3d\fP searches through a PDB file looking for residues containing
+5- or 6-membered rings, then produces a Raster3D output file of ring-filling
+triangles.
+
+\fIrings3d\fP matches residue types from an internal list of residue and
+atom names. It will fail to find residues not in its list, and fail to
+recognize atoms with non-standard names.
+.PP
+.SH EXAMPLES
+.PP
+render a DNA molecule with the bases filled in:
+.PP
+ cat $R3D_LIB/dna.colours dna.pdb | rods -radius 0.05 > temp.1
+ rings3d -bases < dna.pdb > temp.2
+ cat temp.1 temp.2 | render -tiff dna.tiff
+.SH OPTIONS
+
+.B "-bases"
+.PP
+Fills in purine and pyrimidine rings from A C G T U residues.
+
+.B "-protein"
+.PP
+Fills in sidechain rings of HIS PHE TRP and TYR residues.
+
+.B "-sugars"
+.PP
+[This is the default] Fills in pyranose rings of GAL GLC NAG NGA MAN SIA
+residues.
+
+.SH BUGS
+.B limited residue types
+.PP
+The database of residue types should be kept externally, so you don't
+have to rebuild the program to add a new type.
+There should be an option to search for ring systems in un-recognized
+residue types.
+.B crinkled planes
+.PP
+There should be an option to do a least-squares best plane through
+supposedly flat rings. Then again, seeing a crease in a "flat" ring
+may force people to consider whether their planarity restraints are
+tight enough.
+
+.SH SOURCE
+.B anonymous ftp site:
+ ftp.bmsc.washington.edu
+
+.B web URL:
+ http://www.bmsc.washington.edu/raster3d/raster3d.html
+
+.B contact:
+ Ethan A Merritt
+ Dept of Biological Structure Box 357742
+ University of Washington, Seattle WA 98195
+ merritt at u.washington.edu
+
+.SH SEE ALSO
+Raster3D(l)
+.PP
+.SH AUTHORS
+
+Ethan A Merritt.
+.PP
+This manual page was written by Nelson A. de Oliveira <naoliv at gmail.com>,
+for the Debian project (but may be used by others).
Added: trunk/packages/raster3d/trunk/debian/rules
===================================================================
--- trunk/packages/raster3d/trunk/debian/rules (rev 0)
+++ trunk/packages/raster3d/trunk/debian/rules 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,22 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/rules/simple-patchsys.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/makefile.mk
+
+DEB_DESTDIR = $(CURDIR)/debian/tmp
+DEB_MAKE_CLEAN_TARGET := clean
+DEB_MAKE_INSTALL_TARGET := install prefix=$(DEB_DESTDIR)
+DEB_INSTALL_CHANGELOGS_raster3d := CHANGELOG
+DEB_INSTALL_DOCS_ALL :=
+DEB_COMPRESS_EXCLUDE := .pdb .r3d .mol
+
+cleanbuilddir::
+ rm -f debian/diffs.tar
+
+makebuilddir/raster3d::
+ mkdir debian/tmp
+ cd debian/patches/ && tar -cf ../diffs.tar * || true
+
+configure/raster3d::
+ $(MAKE) linux-gfortran
Property changes on: trunk/packages/raster3d/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/raster3d/trunk/debian/watch
===================================================================
--- trunk/packages/raster3d/trunk/debian/watch (rev 0)
+++ trunk/packages/raster3d/trunk/debian/watch 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,3 @@
+version=3
+opts="dversionmangle=s/\+.*//" \
+http://www.bmsc.washington.edu/raster3d/Raster3D_(.*)\.tar\.gz
Added: trunk/packages/raster3d/trunk/debian/wrappers/normal3d
===================================================================
--- trunk/packages/raster3d/trunk/debian/wrappers/normal3d (rev 0)
+++ trunk/packages/raster3d/trunk/debian/wrappers/normal3d 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,7 @@
+#!/bin/sh
+if [ "$R3D_LIB" = "" ]
+then
+ export R3D_LIB=/usr/share/raster3d/materials
+fi
+
+/usr/lib/raster3d/normal3d.real "$@"
Added: trunk/packages/raster3d/trunk/debian/wrappers/render
===================================================================
--- trunk/packages/raster3d/trunk/debian/wrappers/render (rev 0)
+++ trunk/packages/raster3d/trunk/debian/wrappers/render 2008-02-24 03:33:37 UTC (rev 1461)
@@ -0,0 +1,7 @@
+#!/bin/sh
+if [ "$R3D_LIB" = "" ]
+then
+ export R3D_LIB=/usr/share/raster3d/materials
+fi
+
+/usr/lib/raster3d/render.real "$@"
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