--- hmmer-2.3.2.orig/debian/hmmer.NEWS +++ hmmer-2.3.2/debian/hmmer.NEWS @@ -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 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 Tue, 08 Aug 2006 23:07:12 -0300 --- hmmer-2.3.2.orig/debian/hmmer-pvm.README.Debian +++ hmmer-2.3.2/debian/hmmer-pvm.README.Debian @@ -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 Tue, 08 Aug 2006 23:07:12 -0300 --- hmmer-2.3.2.orig/debian/hmmer-pvm.1 +++ hmmer-2.3.2/debian/hmmer-pvm.1 @@ -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 , +for the Debian project (but may be used by others). --- hmmer-2.3.2.orig/debian/hmmer.install +++ hmmer-2.3.2/debian/hmmer.install @@ -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 --- hmmer-2.3.2.orig/debian/hmmer-pvm.manpages +++ hmmer-2.3.2/debian/hmmer-pvm.manpages @@ -0,0 +1 @@ +debian/hmmer-pvm.1 --- hmmer-2.3.2.orig/debian/copyright +++ hmmer-2.3.2/debian/copyright @@ -0,0 +1,29 @@ +This package was debianized by John Lapeyre 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 + +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'. + --- hmmer-2.3.2.orig/debian/watch +++ hmmer-2.3.2/debian/watch @@ -0,0 +1,2 @@ +version=3 +ftp://selab.janelia.org/pub/software/hmmer/CURRENT/hmmer-([0-9\.]*)\.tar\.gz --- hmmer-2.3.2.orig/debian/hmmer-doc.doc-base +++ hmmer-2.3.2/debian/hmmer-doc.doc-base @@ -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: Science/Biology + +Format: PDF +Files: /usr/share/doc/hmmer-doc/Userguide.pdf.gz --- hmmer-2.3.2.orig/debian/rules +++ hmmer-2.3.2/debian/rules @@ -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 --- hmmer-2.3.2.orig/debian/README.Debian +++ hmmer-2.3.2/debian/README.Debian @@ -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 Tue, 08 Aug 2006 23:07:12 -0300 --- hmmer-2.3.2.orig/debian/hmmer-pvm.install +++ hmmer-2.3.2/debian/hmmer-pvm.install @@ -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 --- hmmer-2.3.2.orig/debian/control +++ hmmer-2.3.2/debian/control @@ -0,0 +1,62 @@ +Source: hmmer +Section: science +Priority: optional +Maintainer: Debian-Med Packaging Team +DM-Upload-Allowed: yes +Uploaders: Matthew Vernon , + Nelson A. de Oliveira , + Andreas Tille , + Charles Plessy +Build-Depends: cdbs, debhelper (>= 5), pvm-dev, autotools-dev +Standards-Version: 3.8.0 +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 +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Recommends: biosquid +Suggests: hmmer-doc (>= ${source:Version}), 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. + +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. + +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. --- hmmer-2.3.2.orig/debian/docs +++ hmmer-2.3.2/debian/docs @@ -0,0 +1 @@ +NOTES --- hmmer-2.3.2.orig/debian/hmmer-pvm.links +++ hmmer-2.3.2/debian/hmmer-pvm.links @@ -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 --- hmmer-2.3.2.orig/debian/hmmer-doc.docs +++ hmmer-2.3.2/debian/hmmer-doc.docs @@ -0,0 +1,2 @@ +Userguide.pdf +tutorial/ --- hmmer-2.3.2.orig/debian/compat +++ hmmer-2.3.2/debian/compat @@ -0,0 +1 @@ +5 --- hmmer-2.3.2.orig/debian/changelog +++ hmmer-2.3.2/debian/changelog @@ -0,0 +1,93 @@ +hmmer (2.3.2-5) unstable; urgency=low + + * Changed the doc-base section according to the new policy. + * debian/control: + - Added myself as Uploader. + - Increased priority to `optional' + - Standards-Version: 3.8.0 (no changes needed) + + -- Charles Plessy Sun, 06 Jul 2008 23:49:23 +0900 + +hmmer (2.3.2-4) unstable; urgency=low + + * Moved Homepage tag from long description to tags + * Removed XB-Tag because it is actually not used by debtags + * Added myself as Uploader + * Standards-Version: 3.7.3 (no changes needed) + * Added Vcs-Browser, Vcs-Svn + * DM-Upload-Allowed: yes + + -- Andreas Tille Tue, 26 Feb 2008 20:40:17 +0100 + +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 ; + * Downgraded biosquid to recommends. + + -- Nelson A. de Oliveira 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 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 Tue, 15 Aug 2006 17:30:32 -0300 + +hmmer (2.1.4) unstable; urgency=low + + * Change section to science + + -- Matthew Vernon 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 Mon, 09 Apr 2001 16:12:21 +0100 + +hmmer (2.1.2) unstable; urgency=low + + * New maintainer + + -- Matthew Vernon Tue, 07 Dec 1999 16:30:35 +0000 + +hmmer (2.1.1-1) unstable; urgency=low + + * New upstream version. + + -- John Lapeyre Tue, 30 Mar 1999 16:50:05 -0700 + +hmmer (2.0-1) unstable; urgency=low + + * Initial Release. + + -- John Lapeyre Thu, 13 Aug 1998 21:48:53 -0700