[med-svn] r11604 - trunk/packages/hmmer2/trunk/debian
Laszlo Kajan
lkajan-guest at alioth.debian.org
Fri Jul 6 17:14:52 UTC 2012
Author: lkajan-guest
Date: 2012-07-06 17:14:52 +0000 (Fri, 06 Jul 2012)
New Revision: 11604
Added:
trunk/packages/hmmer2/trunk/debian/upstream
Removed:
trunk/packages/hmmer2/trunk/debian/upstream-metadata.yaml
Modified:
trunk/packages/hmmer2/trunk/debian/README.Debian
trunk/packages/hmmer2/trunk/debian/changelog
trunk/packages/hmmer2/trunk/debian/compat
trunk/packages/hmmer2/trunk/debian/control
trunk/packages/hmmer2/trunk/debian/hmmer-doc.doc-base
trunk/packages/hmmer2/trunk/debian/hmmer-pvm.1
trunk/packages/hmmer2/trunk/debian/hmmer-pvm.README.Debian
trunk/packages/hmmer2/trunk/debian/hmmer-pvm.install
trunk/packages/hmmer2/trunk/debian/hmmer-pvm.links
trunk/packages/hmmer2/trunk/debian/hmmer-pvm.manpages
trunk/packages/hmmer2/trunk/debian/hmmer.install
trunk/packages/hmmer2/trunk/debian/watch
Log:
Essentially s/hmm/hmm2/ in files in debian/
Modified: trunk/packages/hmmer2/trunk/debian/README.Debian
===================================================================
--- trunk/packages/hmmer2/trunk/debian/README.Debian 2012-07-06 17:13:27 UTC (rev 11603)
+++ trunk/packages/hmmer2/trunk/debian/README.Debian 2012-07-06 17:14:52 UTC (rev 11604)
@@ -1,7 +1,7 @@
-hmmer for Debian
-----------------
+hmmer2 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.
+This hmmer2 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
@@ -10,6 +10,6 @@
The HMMER programs are tested when we assemble our binary packages in our build
network, using the standard upstream tests. You can consult the results in the
-build logs: ‘http://buildd.debian.org/hmmer’.
+build logs: ‘http://buildd.debian.org/hmmer2’.
-- Charles Plessy <plessy at debian.org> Wed, 16 Dec 2009 13:52:24 +0900
Modified: trunk/packages/hmmer2/trunk/debian/changelog
===================================================================
--- trunk/packages/hmmer2/trunk/debian/changelog 2012-07-06 17:13:27 UTC (rev 11603)
+++ trunk/packages/hmmer2/trunk/debian/changelog 2012-07-06 17:14:52 UTC (rev 11604)
@@ -1,5 +1,6 @@
-hmmer (2.3.2-6) UNRELEASED; urgency=low
+hmmer2 (2.3.2-1) UNRELEASED; urgency=low
+ [Charles Plessy]
* Enabled upstream checks in debian/rules.
* Documented how the package is tested in debian/README.Debian
* Switched Debhelper to mode 7 (debian/compat, debian/control).
@@ -7,6 +8,23 @@
* Checked conformance with Policy 3.8.3 and incremented Standards-Version
in debian/control to reflect it.
+ [Laszlo Kajan]
+ * Renaming hmmer version 2 to hmmer2 in order to allow coexistence with
+ hmmer (>=3) in wheezy.
+ * Renaming binaries (s/hmm/hmm2/):
+
+ hmmalign => hmm2align
+ hmmbuild => hmm2build
+ hmmcalibrate => hmm2calibrate
+ hmmconvert => hmm2convert
+ hmmemit => hmm2emit
+ hmmfetch => hmm2fetch
+ hmmindex => hmm2index
+ hmmpfam => hmm2pfam
+ hmmsearch => hmm2search
+
+ in order to allow coexistence with those from hmmer (>=3).
+
-- Charles Plessy <plessy at debian.org> Wed, 16 Dec 2009 13:21:02 +0900
hmmer (2.3.2-5) unstable; urgency=low
Modified: trunk/packages/hmmer2/trunk/debian/compat
===================================================================
--- trunk/packages/hmmer2/trunk/debian/compat 2012-07-06 17:13:27 UTC (rev 11603)
+++ trunk/packages/hmmer2/trunk/debian/compat 2012-07-06 17:14:52 UTC (rev 11604)
@@ -1 +1 @@
-7
+8
Modified: trunk/packages/hmmer2/trunk/debian/control
===================================================================
--- trunk/packages/hmmer2/trunk/debian/control 2012-07-06 17:13:27 UTC (rev 11603)
+++ trunk/packages/hmmer2/trunk/debian/control 2012-07-06 17:14:52 UTC (rev 11604)
@@ -1,4 +1,4 @@
-Source: hmmer
+Source: hmmer2
Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
@@ -6,18 +6,19 @@
Uploaders: Matthew Vernon <matthew at debian.org>,
Nelson A. de Oliveira <naoliv at debian.org>,
Andreas Tille <tille at debian.org>,
- Charles Plessy <plessy at debian.org>
-Build-Depends: cdbs, debhelper (>= 7), pvm-dev, autotools-dev
-Standards-Version: 3.8.3
+ Charles Plessy <plessy at debian.org>,
+ Laszlo Kajan <lkajan at rostlab.org>
+Build-Depends: cdbs, debhelper (>= 8), pvm-dev, autotools-dev
+Standards-Version: 3.9.3
Homepage: http://hmmer.janelia.org/
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/hmmer/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/hmmer/trunk/
-Package: hmmer
+Package: hmmer2
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
Recommends: biosquid
-Suggests: hmmer-doc (>= ${source:Version}), hmmer-pvm (>= ${binary:Version})
+Suggests: hmmer2-doc (>= ${source:Version}), hmmer2-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
@@ -28,10 +29,10 @@
a sequence database to find (and/or align) additional homologues of the
sequence family.
-Package: hmmer-pvm
+Package: hmmer2-pvm
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}, pvm
-Suggests: hmmer-doc (>= ${binary:Version})
+Suggests: hmmer2-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
@@ -44,11 +45,11 @@
.
This package contains HMMER programs compiled with PVM support.
-Package: hmmer-doc
+Package: hmmer2-doc
Section: doc
Architecture: all
Depends: ${shlibs:Depends}, ${misc:Depends}
-Recommends: hmmer (>= ${source:Version}), xpdf-reader | pdf-viewer
+Recommends: hmmer2 (>= ${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
@@ -59,4 +60,4 @@
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.
+ This package contains documents and example files for the hmmer2 package.
Modified: trunk/packages/hmmer2/trunk/debian/hmmer-doc.doc-base
===================================================================
--- trunk/packages/hmmer2/trunk/debian/hmmer-doc.doc-base 2012-07-06 17:13:27 UTC (rev 11603)
+++ trunk/packages/hmmer2/trunk/debian/hmmer-doc.doc-base 2012-07-06 17:14:52 UTC (rev 11604)
@@ -1,4 +1,4 @@
-Document: hmmer
+Document: hmmer2
Title: Hmmer 2.3.2 Userguide
Author: Sean Eddy
Abstract: HMMER is an implementation of profile hidden Markov model methods for
@@ -12,4 +12,4 @@
Section: Science/Biology
Format: PDF
-Files: /usr/share/doc/hmmer-doc/Userguide.pdf.gz
+Files: /usr/share/doc/hmmer2-doc/Userguide.pdf.gz
Modified: trunk/packages/hmmer2/trunk/debian/hmmer-pvm.1
===================================================================
--- trunk/packages/hmmer2/trunk/debian/hmmer-pvm.1 2012-07-06 17:13:27 UTC (rev 11603)
+++ trunk/packages/hmmer2/trunk/debian/hmmer-pvm.1 2012-07-06 17:14:52 UTC (rev 11604)
@@ -1,6 +1,6 @@
.TH HMMER-PVM 1 "Tue, 08 Aug 2006 20:00:00 -0300"
.SH NAME
-hmmer-pvm \- HMMER utilities for PVM clusters
+hmmer2-pvm \- HMMER utilities for PVM clusters
.SH DESCRIPTION
Information on how to use the programs
.B hmmcalibrate-pvm
@@ -8,10 +8,11 @@
.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".
+is available on the section "Configuring a PVM cluster for HMMER" (page 15) at the User's Guide (/usr/share/doc/hmmer2-doc/Userguide.pdf.gz), installed with the package "hmmer2-doc".
.PP
.SH SEE ALSO
-.BR hmmer (1).
+.BR hmmer2 (1),
+.BR hmmer (1)
.SH AUTHOR
HMMER was written by Sean Eddy.
.PP
Modified: trunk/packages/hmmer2/trunk/debian/hmmer-pvm.README.Debian
===================================================================
--- trunk/packages/hmmer2/trunk/debian/hmmer-pvm.README.Debian 2012-07-06 17:13:27 UTC (rev 11603)
+++ trunk/packages/hmmer2/trunk/debian/hmmer-pvm.README.Debian 2012-07-06 17:14:52 UTC (rev 11604)
@@ -1,8 +1,8 @@
-hmmer-pvm for Debian
+hmmer2-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
+ at the User's Guide (/usr/share/doc/hmmer2-doc/Userguide.pdf.gz), installed with the package "hmmer2-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
Modified: trunk/packages/hmmer2/trunk/debian/hmmer-pvm.install
===================================================================
--- trunk/packages/hmmer2/trunk/debian/hmmer-pvm.install 2012-07-06 17:13:27 UTC (rev 11603)
+++ trunk/packages/hmmer2/trunk/debian/hmmer-pvm.install 2012-07-06 17:14:52 UTC (rev 11604)
@@ -1,3 +1,3 @@
-debian/tmp/bin/hmmcalibrate-pvm usr/bin
-debian/tmp/bin/hmmpfam-pvm usr/bin
-debian/tmp/bin/hmmsearch-pvm usr/bin
+debian/tmp/bin/hmm2calibrate-pvm usr/bin
+debian/tmp/bin/hmm2pfam-pvm usr/bin
+debian/tmp/bin/hmm2search-pvm usr/bin
Modified: trunk/packages/hmmer2/trunk/debian/hmmer-pvm.links
===================================================================
--- trunk/packages/hmmer2/trunk/debian/hmmer-pvm.links 2012-07-06 17:13:27 UTC (rev 11603)
+++ trunk/packages/hmmer2/trunk/debian/hmmer-pvm.links 2012-07-06 17:14:52 UTC (rev 11604)
@@ -1,3 +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
+usr/share/man/man1/hmmer2-pvm.1.gz usr/share/man/man1/hmm2calibrate-pvm.1.gz
+usr/share/man/man1/hmmer2-pvm.1.gz usr/share/man/man1/hmm2pfam-pvm.1.gz
+usr/share/man/man1/hmmer2-pvm.1.gz usr/share/man/man1/hmm2search-pvm.1.gz
Modified: trunk/packages/hmmer2/trunk/debian/hmmer-pvm.manpages
===================================================================
--- trunk/packages/hmmer2/trunk/debian/hmmer-pvm.manpages 2012-07-06 17:13:27 UTC (rev 11603)
+++ trunk/packages/hmmer2/trunk/debian/hmmer-pvm.manpages 2012-07-06 17:14:52 UTC (rev 11604)
@@ -1 +1 @@
-debian/hmmer-pvm.1
+debian/hmmer2-pvm.1
Modified: trunk/packages/hmmer2/trunk/debian/hmmer.install
===================================================================
--- trunk/packages/hmmer2/trunk/debian/hmmer.install 2012-07-06 17:13:27 UTC (rev 11603)
+++ trunk/packages/hmmer2/trunk/debian/hmmer.install 2012-07-06 17:14:52 UTC (rev 11604)
@@ -1,10 +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
+debian/tmp/bin/hmm2align usr/bin
+debian/tmp/bin/hmm2build usr/bin
+debian/tmp/bin/hmm2calibrate usr/bin
+debian/tmp/bin/hmm2convert usr/bin
+debian/tmp/bin/hmm2emit usr/bin
+debian/tmp/bin/hmm2fetch usr/bin
+debian/tmp/bin/hmm2index usr/bin
+debian/tmp/bin/hmm2pfam usr/bin
+debian/tmp/bin/hmm2search usr/bin
Copied: trunk/packages/hmmer2/trunk/debian/upstream (from rev 11603, trunk/packages/hmmer2/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/hmmer2/trunk/debian/upstream (rev 0)
+++ trunk/packages/hmmer2/trunk/debian/upstream 2012-07-06 17:14:52 UTC (rev 11604)
@@ -0,0 +1,15 @@
+Contact: http://selab.janelia.org/people/eddys/contact.html
+DOI: 10.1093/bioinformatics/14.9.755
+Name: HMMER
+Homepage: http://hmmer.janelia.org
+PMID: 9918945
+Reference:
+ Author: Eddy, SR
+ Title: Profile hidden Markov models
+ Journal: Bioinformatics
+ Volume: 14
+ Number: 9
+ Pages: 755-763
+ Year: 1998
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/14/9/755
+Watch: ftp://selab.janelia.org/pub/software/hmmer/CURRENT/hmmer-([0-9\.]*)\.tar\.gz
Deleted: trunk/packages/hmmer2/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/hmmer2/trunk/debian/upstream-metadata.yaml 2012-07-06 17:13:27 UTC (rev 11603)
+++ trunk/packages/hmmer2/trunk/debian/upstream-metadata.yaml 2012-07-06 17:14:52 UTC (rev 11604)
@@ -1,15 +0,0 @@
-Contact: http://selab.janelia.org/people/eddys/contact.html
-DOI: 10.1093/bioinformatics/14.9.755
-Name: HMMER
-Homepage: http://hmmer.janelia.org
-PMID: 9918945
-Reference:
- Author: Eddy, SR
- Title: Profile hidden Markov models
- Journal: Bioinformatics
- Volume: 14
- Number: 9
- Pages: 755-763
- Year: 1998
- URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/14/9/755
-Watch: ftp://selab.janelia.org/pub/software/hmmer/CURRENT/hmmer-([0-9\.]*)\.tar\.gz
Modified: trunk/packages/hmmer2/trunk/debian/watch
===================================================================
--- trunk/packages/hmmer2/trunk/debian/watch 2012-07-06 17:13:27 UTC (rev 11603)
+++ trunk/packages/hmmer2/trunk/debian/watch 2012-07-06 17:14:52 UTC (rev 11604)
@@ -1,2 +1,2 @@
version=3
-ftp://selab.janelia.org/pub/software/hmmer/CURRENT/hmmer-([0-9\.]*)\.tar\.gz
+ftp://selab.janelia.org/pub/software/hmmer/2.3.2/hmmer-([0-9.]+)\.tar\.gz
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