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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> @@ -6,18 +6,19 @@ Uploaders: Matthew Vernon <[email protected]>, Nelson A. de Oliveira <[email protected]>, Andreas Tille <[email protected]>, - Charles Plessy <[email protected]> -Build-Depends: cdbs, debhelper (>= 7), pvm-dev, autotools-dev -Standards-Version: 3.8.3 + Charles Plessy <[email protected]>, + Laszlo Kajan <[email protected]> +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 <[email protected]> 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
