[med-svn] r1475 - in trunk/packages/hmmer: . tags tags/2.3.2-3 tags/2.3.2-3/debian trunk/debian

naoliv at alioth.debian.org naoliv at alioth.debian.org
Tue Feb 26 20:12:10 UTC 2008


Author: naoliv
Date: 2008-02-26 20:12:09 +0000 (Tue, 26 Feb 2008)
New Revision: 1475

Added:
   trunk/packages/hmmer/branches/
   trunk/packages/hmmer/tags/2.3.2-3/
   trunk/packages/hmmer/tags/2.3.2-3/debian/
   trunk/packages/hmmer/tags/2.3.2-3/debian/README.Debian
   trunk/packages/hmmer/tags/2.3.2-3/debian/changelog
   trunk/packages/hmmer/tags/2.3.2-3/debian/compat
   trunk/packages/hmmer/tags/2.3.2-3/debian/control
   trunk/packages/hmmer/tags/2.3.2-3/debian/copyright
   trunk/packages/hmmer/tags/2.3.2-3/debian/docs
   trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer-doc.doc-base
   trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer-doc.docs
   trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer-pvm.1
   trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer-pvm.README.Debian
   trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer-pvm.install
   trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer-pvm.links
   trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer-pvm.manpages
   trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer.NEWS
   trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer.install
   trunk/packages/hmmer/tags/2.3.2-3/debian/rules
   trunk/packages/hmmer/tags/2.3.2-3/debian/watch
   trunk/packages/hmmer/trunk/
Removed:
   trunk/packages/hmmer/tags/debian/
Modified:
   trunk/packages/hmmer/trunk/debian/changelog
Log:
Fixing tags and hmmer (just to don't say "Fixing Andreas' mess") :-P


Added: trunk/packages/hmmer/tags/2.3.2-3/debian/README.Debian
===================================================================
--- trunk/packages/hmmer/tags/2.3.2-3/debian/README.Debian	                        (rev 0)
+++ trunk/packages/hmmer/tags/2.3.2-3/debian/README.Debian	2008-02-26 20:12:09 UTC (rev 1475)
@@ -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/2.3.2-3/debian/changelog
===================================================================
--- trunk/packages/hmmer/tags/2.3.2-3/debian/changelog	                        (rev 0)
+++ trunk/packages/hmmer/tags/2.3.2-3/debian/changelog	2008-02-26 20:12:09 UTC (rev 1475)
@@ -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/2.3.2-3/debian/compat
===================================================================
--- trunk/packages/hmmer/tags/2.3.2-3/debian/compat	                        (rev 0)
+++ trunk/packages/hmmer/tags/2.3.2-3/debian/compat	2008-02-26 20:12:09 UTC (rev 1475)
@@ -0,0 +1 @@
+5

Added: trunk/packages/hmmer/tags/2.3.2-3/debian/control
===================================================================
--- trunk/packages/hmmer/tags/2.3.2-3/debian/control	                        (rev 0)
+++ trunk/packages/hmmer/tags/2.3.2-3/debian/control	2008-02-26 20:12:09 UTC (rev 1475)
@@ -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/2.3.2-3/debian/copyright
===================================================================
--- trunk/packages/hmmer/tags/2.3.2-3/debian/copyright	                        (rev 0)
+++ trunk/packages/hmmer/tags/2.3.2-3/debian/copyright	2008-02-26 20:12:09 UTC (rev 1475)
@@ -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/2.3.2-3/debian/docs
===================================================================
--- trunk/packages/hmmer/tags/2.3.2-3/debian/docs	                        (rev 0)
+++ trunk/packages/hmmer/tags/2.3.2-3/debian/docs	2008-02-26 20:12:09 UTC (rev 1475)
@@ -0,0 +1 @@
+NOTES

Added: trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer-doc.doc-base
===================================================================
--- trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer-doc.doc-base	                        (rev 0)
+++ trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer-doc.doc-base	2008-02-26 20:12:09 UTC (rev 1475)
@@ -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/2.3.2-3/debian/hmmer-doc.docs
===================================================================
--- trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer-doc.docs	                        (rev 0)
+++ trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer-doc.docs	2008-02-26 20:12:09 UTC (rev 1475)
@@ -0,0 +1,2 @@
+Userguide.pdf
+tutorial/

Added: trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer-pvm.1
===================================================================
--- trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer-pvm.1	                        (rev 0)
+++ trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer-pvm.1	2008-02-26 20:12:09 UTC (rev 1475)
@@ -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/2.3.2-3/debian/hmmer-pvm.README.Debian
===================================================================
--- trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer-pvm.README.Debian	                        (rev 0)
+++ trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer-pvm.README.Debian	2008-02-26 20:12:09 UTC (rev 1475)
@@ -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/2.3.2-3/debian/hmmer-pvm.install
===================================================================
--- trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer-pvm.install	                        (rev 0)
+++ trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer-pvm.install	2008-02-26 20:12:09 UTC (rev 1475)
@@ -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/2.3.2-3/debian/hmmer-pvm.links
===================================================================
--- trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer-pvm.links	                        (rev 0)
+++ trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer-pvm.links	2008-02-26 20:12:09 UTC (rev 1475)
@@ -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/2.3.2-3/debian/hmmer-pvm.manpages
===================================================================
--- trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer-pvm.manpages	                        (rev 0)
+++ trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer-pvm.manpages	2008-02-26 20:12:09 UTC (rev 1475)
@@ -0,0 +1 @@
+debian/hmmer-pvm.1

Added: trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer.NEWS
===================================================================
--- trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer.NEWS	                        (rev 0)
+++ trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer.NEWS	2008-02-26 20:12:09 UTC (rev 1475)
@@ -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/2.3.2-3/debian/hmmer.install
===================================================================
--- trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer.install	                        (rev 0)
+++ trunk/packages/hmmer/tags/2.3.2-3/debian/hmmer.install	2008-02-26 20:12:09 UTC (rev 1475)
@@ -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/2.3.2-3/debian/rules
===================================================================
--- trunk/packages/hmmer/tags/2.3.2-3/debian/rules	                        (rev 0)
+++ trunk/packages/hmmer/tags/2.3.2-3/debian/rules	2008-02-26 20:12:09 UTC (rev 1475)
@@ -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/2.3.2-3/debian/rules
___________________________________________________________________
Name: svn:executable
   + *

Added: trunk/packages/hmmer/tags/2.3.2-3/debian/watch
===================================================================
--- trunk/packages/hmmer/tags/2.3.2-3/debian/watch	                        (rev 0)
+++ trunk/packages/hmmer/tags/2.3.2-3/debian/watch	2008-02-26 20:12:09 UTC (rev 1475)
@@ -0,0 +1,2 @@
+version=3
+ftp://selab.janelia.org/pub/software/hmmer/CURRENT/hmmer-([0-9\.]*)\.tar\.gz

Copied: trunk/packages/hmmer/trunk (from rev 1474, trunk/packages/hmmer/tags)

Modified: trunk/packages/hmmer/trunk/debian/changelog
===================================================================
--- trunk/packages/hmmer/tags/debian/changelog	2008-02-26 19:45:35 UTC (rev 1474)
+++ trunk/packages/hmmer/trunk/debian/changelog	2008-02-26 20:12:09 UTC (rev 1475)
@@ -1,4 +1,4 @@
-hmmer (2.3.2-4) unstable; urgency=low
+hmmer (2.3.2-4) UNRELEASED; urgency=low
 
   * Moved Homepage tag from long description to tags
   * Removed XB-Tag because it is actually not used by debtags




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