[med-svn] r1473 - in trunk/packages: . hmmer hmmer/tags hmmer/tags/debian
tille at alioth.debian.org
tille at alioth.debian.org
Tue Feb 26 19:38:54 UTC 2008
Author: tille
Date: 2008-02-26 19:38:51 +0000 (Tue, 26 Feb 2008)
New Revision: 1473
Added:
trunk/packages/hmmer/
trunk/packages/hmmer/tags/
trunk/packages/hmmer/tags/debian/
trunk/packages/hmmer/tags/debian/README.Debian
trunk/packages/hmmer/tags/debian/changelog
trunk/packages/hmmer/tags/debian/compat
trunk/packages/hmmer/tags/debian/control
trunk/packages/hmmer/tags/debian/copyright
trunk/packages/hmmer/tags/debian/docs
trunk/packages/hmmer/tags/debian/hmmer-doc.doc-base
trunk/packages/hmmer/tags/debian/hmmer-doc.docs
trunk/packages/hmmer/tags/debian/hmmer-pvm.1
trunk/packages/hmmer/tags/debian/hmmer-pvm.README.Debian
trunk/packages/hmmer/tags/debian/hmmer-pvm.install
trunk/packages/hmmer/tags/debian/hmmer-pvm.links
trunk/packages/hmmer/tags/debian/hmmer-pvm.manpages
trunk/packages/hmmer/tags/debian/hmmer.NEWS
trunk/packages/hmmer/tags/debian/hmmer.install
trunk/packages/hmmer/tags/debian/rules
trunk/packages/hmmer/tags/debian/watch
Log:
Putting hmmer packaging under version control
Added: trunk/packages/hmmer/tags/debian/README.Debian
===================================================================
--- trunk/packages/hmmer/tags/debian/README.Debian (rev 0)
+++ trunk/packages/hmmer/tags/debian/README.Debian 2008-02-26 19:38:51 UTC (rev 1473)
@@ -0,0 +1,6 @@
+hmmer for Debian
+----------------
+
+This hmmer package has been built with POSIX multithreading support (--enable-threads), Large File Support (--enable-lfs) and Parallel Virtual Machine (--enable-pvm) enabled.
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com> Tue, 08 Aug 2006 23:07:12 -0300
Added: trunk/packages/hmmer/tags/debian/changelog
===================================================================
--- trunk/packages/hmmer/tags/debian/changelog (rev 0)
+++ trunk/packages/hmmer/tags/debian/changelog 2008-02-26 19:38:51 UTC (rev 1473)
@@ -0,0 +1,72 @@
+hmmer (2.3.2-3) unstable; urgency=low
+
+ * Updated hmmer homepage (Closes: #435396). Thanks to Charles Plessy;
+ * Updated watch file;
+ * Moved Matthew Vernon to Uploaders and set Maintainer to Debian-Med
+ Packaging Team <debian-med-packaging at lists.alioth.debian.org>;
+ * Downgraded biosquid to recommends.
+
+ -- Nelson A. de Oliveira <naoliv at debian.org> Tue, 31 Jul 2007 15:15:23 -0300
+
+hmmer (2.3.2-2) unstable; urgency=medium
+
+ * Changed my email address;
+ * Changing priority to extra, instead optional (hmmer has a dependency on
+ pvm and libpmv3 -- Policy 2.5);
+ * Added tags on debian/control;
+ * Medium urgency to get the package with the correct priority on Etch.
+
+ -- Nelson A. de Oliveira <naoliv at debian.org> Wed, 6 Dec 2006 16:27:06 -0200
+
+hmmer (2.3.2-1) unstable; urgency=low
+
+ * New upstream version (Closes: #261293);
+ * Documentation is split in a new package (Closes: #233374, #175481);
+ * "getseq" is not shipped anymore with hmmer, since it was renamed to
+ "sfetch" (Closes: #197658);
+ * New package hmmer-pvm, with PVM enabled binaries;
+ * The package is again non-Debian native;
+ * Using CDBS;
+ * Using debhelper compatibility level 5;
+ * Updated Standards-Version to 3.7.2;
+ * Added doc-base and watch file;
+ * Updated copyright file;
+ * Added me as co-maintainer.
+ From Matthew Vernon:
+ "If you're keen to take hmmer, take it; I'm writing up my thesis at the
+ moment, so my time for Debian is somewhat limited; I took on hmmer
+ because it was orphaned at the time, and I wanted it to stay in the
+ distribution."
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com> Tue, 15 Aug 2006 17:30:32 -0300
+
+hmmer (2.1.4) unstable; urgency=low
+
+ * Change section to science
+
+ -- Matthew Vernon <matthew at debian.org> Tue, 10 Apr 2001 02:51:17 +0100
+
+hmmer (2.1.3) unstable; urgency=low
+
+ * Move from /usr/man to /usr/share/man (closes: #91171)
+ * Move from /usr/doc to /usr/share/doc (closes: #91494)
+
+ -- Matthew Vernon <matthew at debian.org> Mon, 09 Apr 2001 16:12:21 +0100
+
+hmmer (2.1.2) unstable; urgency=low
+
+ * New maintainer
+
+ -- Matthew Vernon <matthew at debian.org> Tue, 07 Dec 1999 16:30:35 +0000
+
+hmmer (2.1.1-1) unstable; urgency=low
+
+ * New upstream version.
+
+ -- John Lapeyre <lapeyre at physics.arizona.edu> Tue, 30 Mar 1999 16:50:05 -0700
+
+hmmer (2.0-1) unstable; urgency=low
+
+ * Initial Release.
+
+ -- John Lapeyre <lapeyre at physics.arizona.edu> Thu, 13 Aug 1998 21:48:53 -0700
Added: trunk/packages/hmmer/tags/debian/compat
===================================================================
--- trunk/packages/hmmer/tags/debian/compat (rev 0)
+++ trunk/packages/hmmer/tags/debian/compat 2008-02-26 19:38:51 UTC (rev 1473)
@@ -0,0 +1 @@
+5
Added: trunk/packages/hmmer/tags/debian/control
===================================================================
--- trunk/packages/hmmer/tags/debian/control (rev 0)
+++ trunk/packages/hmmer/tags/debian/control 2008-02-26 19:38:51 UTC (rev 1473)
@@ -0,0 +1,64 @@
+Source: hmmer
+Section: science
+Priority: extra
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Matthew Vernon <matthew at debian.org>, Nelson A. de Oliveira <naoliv at debian.org>
+Build-Depends: cdbs, debhelper (>= 5), pvm-dev, autotools-dev
+Standards-Version: 3.7.2
+
+Package: hmmer
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Recommends: hmmer-doc (>= ${source:Version}), biosquid
+Suggests: hmmer-pvm (>= ${binary:Version})
+Description: profile hidden Markov models for protein sequence analysis
+ HMMER is an implementation of profile hidden Markov model methods for
+ sensitive searches of biological sequence databases using multiple sequence
+ alignments as queries.
+ .
+ Given a multiple sequence alignment as input, HMMER builds a statistical
+ model called a "hidden Markov model" which can then be used as a query into
+ a sequence database to find (and/or align) additional homologues of the
+ sequence family.
+ .
+ Homepage: http://hmmer.janelia.org/
+XB-Tag: field::biology, implemented-in::c, interface::commandline, role::program, scope::utility
+
+Package: hmmer-pvm
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, pvm
+Suggests: hmmer-doc (>= ${binary:Version})
+Description: HMMER programs with PVM (Parallel Virtual Machine) support
+ HMMER is an implementation of profile hidden Markov model methods for
+ sensitive searches of biological sequence databases using multiple sequence
+ alignments as queries.
+ .
+ Given a multiple sequence alignment as input, HMMER builds a statistical
+ model called a "hidden Markov model" which can then be used as a query into
+ a sequence database to find (and/or align) additional homologues of the
+ sequence family.
+ .
+ This package contains HMMER programs compiled with PVM support.
+ .
+ Homepage: http://hmmer.janelia.org/
+XB-Tag: field::biology, implemented-in::c, interface::commandline, role::program, scope::utility
+
+Package: hmmer-doc
+Section: doc
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Recommends: hmmer (>= ${source:Version}), xpdf-reader | pdf-viewer
+Description: profile hidden Markov models for protein sequence analysis (docs)
+ HMMER is an implementation of profile hidden Markov model methods for
+ sensitive searches of biological sequence databases using multiple sequence
+ alignments as queries.
+ .
+ Given a multiple sequence alignment as input, HMMER builds a statistical
+ model called a "hidden Markov model" which can then be used as a query into
+ a sequence database to find (and/or align) additional homologues of the
+ sequence family.
+ .
+ This package contains documents and example files for the hmmer package.
+ .
+ Homepage: http://hmmer.janelia.org/
+XB-Tag: devel::doc, devel::examples, field::biology, made-of::data:pdf, role::documentation
Added: trunk/packages/hmmer/tags/debian/copyright
===================================================================
--- trunk/packages/hmmer/tags/debian/copyright (rev 0)
+++ trunk/packages/hmmer/tags/debian/copyright 2008-02-26 19:38:51 UTC (rev 1473)
@@ -0,0 +1,29 @@
+This package was debianized by John Lapeyre <lapeyre at physics.arizona.edu> on
+Thu, 13 Aug 1998 21:48:53 -0700.
+
+It was downloaded from ftp://selab.janelia.org/pub/software/hmmer/
+
+HMMER - Biological sequence analysis with profile hidden Markov models
+Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
+
+Upstream author: Sean Eddy <eddy at genetics.wustl.edu>
+
+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/hmmer/tags/debian/docs
===================================================================
--- trunk/packages/hmmer/tags/debian/docs (rev 0)
+++ trunk/packages/hmmer/tags/debian/docs 2008-02-26 19:38:51 UTC (rev 1473)
@@ -0,0 +1 @@
+NOTES
Added: trunk/packages/hmmer/tags/debian/hmmer-doc.doc-base
===================================================================
--- trunk/packages/hmmer/tags/debian/hmmer-doc.doc-base (rev 0)
+++ trunk/packages/hmmer/tags/debian/hmmer-doc.doc-base 2008-02-26 19:38:51 UTC (rev 1473)
@@ -0,0 +1,15 @@
+Document: hmmer
+Title: Hmmer 2.3.2 Userguide
+Author: Sean Eddy
+Abstract: HMMER is an implementation of profile hidden Markov model methods for
+ sensitive searches of biological sequence databases using multiple sequence
+ alignments as queries.
+ .
+ Given a multiple sequence alignment as input, HMMER builds a statistical
+ model called a "hidden Markov model" which can then be used as a query into
+ a sequence database to find (and/or align) additional homologues of the
+ sequence family.
+Section: Apps/Science
+
+Format: PDF
+Files: /usr/share/doc/hmmer-doc/Userguide.pdf.gz
Added: trunk/packages/hmmer/tags/debian/hmmer-doc.docs
===================================================================
--- trunk/packages/hmmer/tags/debian/hmmer-doc.docs (rev 0)
+++ trunk/packages/hmmer/tags/debian/hmmer-doc.docs 2008-02-26 19:38:51 UTC (rev 1473)
@@ -0,0 +1,2 @@
+Userguide.pdf
+tutorial/
Added: trunk/packages/hmmer/tags/debian/hmmer-pvm.1
===================================================================
--- trunk/packages/hmmer/tags/debian/hmmer-pvm.1 (rev 0)
+++ trunk/packages/hmmer/tags/debian/hmmer-pvm.1 2008-02-26 19:38:51 UTC (rev 1473)
@@ -0,0 +1,19 @@
+.TH HMMER-PVM 1 "Tue, 08 Aug 2006 20:00:00 -0300"
+.SH NAME
+hmmer-pvm \- HMMER utilities for PVM clusters
+.SH DESCRIPTION
+Information on how to use the programs
+.B hmmcalibrate-pvm
+,
+.B hmmpfam-pvm
+and
+.B hmmsearch-pvm
+is available on the section "Configuring a PVM cluster for HMMER" (page 15) at the User's Guide (/usr/share/doc/hmmer-doc/Userguide.pdf.gz), installed with the package "hmmer-doc".
+.PP
+.SH SEE ALSO
+.BR hmmer (1).
+.SH AUTHOR
+HMMER was written by Sean Eddy.
+.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/hmmer/tags/debian/hmmer-pvm.README.Debian
===================================================================
--- trunk/packages/hmmer/tags/debian/hmmer-pvm.README.Debian (rev 0)
+++ trunk/packages/hmmer/tags/debian/hmmer-pvm.README.Debian 2008-02-26 19:38:51 UTC (rev 1473)
@@ -0,0 +1,8 @@
+hmmer-pvm for Debian
+--------------------
+
+ Please, read the section "Configuring a PVM cluster for HMMER" (page 15)
+ at the User's Guide (/usr/share/doc/hmmer-doc/Userguide.pdf.gz), installed with the package "hmmer-doc", to see how to configure properly Hmmer on a PVM
+ cluster.
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com> Tue, 08 Aug 2006 23:07:12 -0300
Added: trunk/packages/hmmer/tags/debian/hmmer-pvm.install
===================================================================
--- trunk/packages/hmmer/tags/debian/hmmer-pvm.install (rev 0)
+++ trunk/packages/hmmer/tags/debian/hmmer-pvm.install 2008-02-26 19:38:51 UTC (rev 1473)
@@ -0,0 +1,3 @@
+debian/tmp/bin/hmmcalibrate-pvm usr/bin
+debian/tmp/bin/hmmpfam-pvm usr/bin
+debian/tmp/bin/hmmsearch-pvm usr/bin
Added: trunk/packages/hmmer/tags/debian/hmmer-pvm.links
===================================================================
--- trunk/packages/hmmer/tags/debian/hmmer-pvm.links (rev 0)
+++ trunk/packages/hmmer/tags/debian/hmmer-pvm.links 2008-02-26 19:38:51 UTC (rev 1473)
@@ -0,0 +1,3 @@
+usr/share/man/man1/hmmer-pvm.1.gz usr/share/man/man1/hmmcalibrate-pvm.1.gz
+usr/share/man/man1/hmmer-pvm.1.gz usr/share/man/man1/hmmpfam-pvm.1.gz
+usr/share/man/man1/hmmer-pvm.1.gz usr/share/man/man1/hmmsearch-pvm.1.gz
Added: trunk/packages/hmmer/tags/debian/hmmer-pvm.manpages
===================================================================
--- trunk/packages/hmmer/tags/debian/hmmer-pvm.manpages (rev 0)
+++ trunk/packages/hmmer/tags/debian/hmmer-pvm.manpages 2008-02-26 19:38:51 UTC (rev 1473)
@@ -0,0 +1 @@
+debian/hmmer-pvm.1
Added: trunk/packages/hmmer/tags/debian/hmmer.NEWS
===================================================================
--- trunk/packages/hmmer/tags/debian/hmmer.NEWS (rev 0)
+++ trunk/packages/hmmer/tags/debian/hmmer.NEWS 2008-02-26 19:38:51 UTC (rev 1473)
@@ -0,0 +1,14 @@
+hmmer (2.3.2-3) unstable; urgency=low
+
+ Hmmer dependency on biosquid has been downgraded to recommends, as there is
+ no need for this upgrade path anymore.
+
+ -- Nelson A. de Oliveira <naoliv at debian.org> Tue, 31 Jul 2007 16:18:00 -0300
+
+hmmer (2.3.2-1) unstable; urgency=low
+
+ Some binaries from the old hmmer (version 2.1.4) have been split between two
+ packages: hmmer and biosquid. To maintain all binaries included on the older
+ hmmer, the new hmmer package depends on biosquid.
+
+ -- Nelson A. de Oliveira <naoliv at gmail.com> Tue, 08 Aug 2006 23:07:12 -0300
Added: trunk/packages/hmmer/tags/debian/hmmer.install
===================================================================
--- trunk/packages/hmmer/tags/debian/hmmer.install (rev 0)
+++ trunk/packages/hmmer/tags/debian/hmmer.install 2008-02-26 19:38:51 UTC (rev 1473)
@@ -0,0 +1,10 @@
+debian/tmp/share usr
+debian/tmp/bin/hmmalign usr/bin
+debian/tmp/bin/hmmbuild usr/bin
+debian/tmp/bin/hmmcalibrate usr/bin
+debian/tmp/bin/hmmconvert usr/bin
+debian/tmp/bin/hmmemit usr/bin
+debian/tmp/bin/hmmfetch usr/bin
+debian/tmp/bin/hmmindex usr/bin
+debian/tmp/bin/hmmpfam usr/bin
+debian/tmp/bin/hmmsearch usr/bin
Added: trunk/packages/hmmer/tags/debian/rules
===================================================================
--- trunk/packages/hmmer/tags/debian/rules (rev 0)
+++ trunk/packages/hmmer/tags/debian/rules 2008-02-26 19:38:51 UTC (rev 1473)
@@ -0,0 +1,7 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/class/autotools.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+
+DEB_CONFIGURE_EXTRA_FLAGS := --enable-threads --enable-lfs --enable-pvm
+DEB_MAKE_INSTALL_TARGET := install prefix=$(CURDIR)/debian/tmp
Property changes on: trunk/packages/hmmer/tags/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/hmmer/tags/debian/watch
===================================================================
--- trunk/packages/hmmer/tags/debian/watch (rev 0)
+++ trunk/packages/hmmer/tags/debian/watch 2008-02-26 19:38:51 UTC (rev 1473)
@@ -0,0 +1,2 @@
+version=3
+ftp://selab.janelia.org/pub/software/hmmer/CURRENT/hmmer-([0-9\.]*)\.tar\.gz
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