debian/0000755000000000000000000000000012247133743007174 5ustar debian/control0000644000000000000000000000373612247133633010606 0ustar Source: hmmer Maintainer: Debian Med Packaging Team Uploaders: Matthew Vernon , Nelson A. de Oliveira , Andreas Tille , Eric Talevich , Tim Booth Section: science Priority: optional Build-Depends: debhelper (>= 9), autotools-dev Standards-Version: 3.9.5 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/hmmer/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/hmmer/trunk/ Homepage: http://hmmer.janelia.org/ Package: hmmer Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: hmmer-doc (>= ${source: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-doc Architecture: all Section: doc Depends: ${shlibs:Depends}, ${misc:Depends} Recommends: hmmer (>= ${source:Version}), evince | 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. debian/hmmer.install0000644000000000000000000000002612214301224011653 0ustar usr/bin usr/share/man debian/rules0000755000000000000000000000114112247132105010240 0ustar #!/usr/bin/make -f # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 %: dh $@ --with autotools_dev ARCH := $(shell dpkg-architecture -qDEB_BUILD_ARCH_CPU) ifeq (amd64,$(ARCH)) DEB_CONFIGURE_EXTRA_FLAGS := --enable-threads --enable-sse else DEB_CONFIGURE_EXTRA_FLAGS := --enable-threads endif override_dh_auto_configure: dh_auto_configure -- $(DEB_CONFIGURE_EXTRA_FLAGS) override_dh_auto_test: make check override_dh_auto_clean: dh_auto_clean rm -f testsuite/esltmp* rm -f easel/testsuite/esltmp* rm -f tutorial/MADE1.hmm.h3? override_dh_compress: dh_compress -Xtutorial/ debian/watch0000644000000000000000000000013312214301224010203 0ustar version=3 ftp://selab.janelia.org/pub/software/hmmer3/CURRENT/hmmer-([0-9\.abc]*)\.tar\.gz debian/hmmer-doc.doc-base0000644000000000000000000000110012214301224012417 0ustar 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 debian/upstream0000644000000000000000000000167412214301224010750 0ustar Contact: http://selab.janelia.org/people/eddys/contact.html Name: HMMER Homepage: http://hmmer.janelia.org Reference: - Author: S. R. Eddy Title: Profile hidden Markov models Journal: Bioinformatics Volume: 14 Number: 9 Pages: 755-763 Year: 1998 DOI: 10.1093/bioinformatics/14.9.755 PMID: 9918945 URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/14/9/755 eprint: http://bioinformatics.oxfordjournals.org/content/14/9/755.full.pdf+html - Author: S. R. Eddy Title: Multiple Alignment Using Hidden Markov Models Journal: Proc. Third Int. Conf. Intelligent Systems for Molecular Biology Volume: 3 Pages: 114-120 Year: 1995 PMID: 7584426 URL: http://www.mendeley.com/research/multiple-alignment-using-hidden-markov-models-1/ Eprint: ftp://selab.janelia.org/pub/publications/Eddy95b/Eddy95b-preprint.pdf Watch: ftp://selab.janelia.org/pub/software/hmmer/CURRENT/hmmer-([0-9\.]*)\.tar\.gz debian/copyright0000644000000000000000000000647612214301224011125 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: HMMER Upstream-Contact: Sean R. Eddy Source: ftp://selab.janelia.org/pub/software/hmmer3/3.0/ Files: * Copyright: 1992-2010 Sean R. Eddy Howard Hughes Medical Institute 1992-2004 Washington University School of Medicine 1992-1994 MRC Laboratory of Molecular Biology License: GPL-3+ Files: easel/* Copyright: 2004-2009 Sean R. Eddy 2006-2009 Howard Hughes Medical Institute License: The-Janelia-Farm-Software-License Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. . 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. . 3. Neither the name of the Howard Hughes Medical Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. . THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, ANY IMPLIED WARRANTIES OF MERCHANTABILITY, NON-INFRINGEMENT, OR FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; REASONABLE ROYALTIES; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Files: debian/* Copyright: 1998 John Lapeyre 1999-2001 Matthew Vernon 2006-2007 Nelson A. de Oliveira 2008-2012 Andreas Tille Charles Plessy 2010 Eric Talevich , Steffen Möller License: GPL-3+ License: GPL-3+ This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License version 3 as published by the Free Software Foundation. . 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-3'. debian/source/0000755000000000000000000000000012203215621010460 5ustar debian/source/format0000644000000000000000000000001411416071110011664 0ustar 3.0 (quilt) debian/README.Debian0000644000000000000000000000075312214301224011223 0ustar hmmer for Debian ---------------- This is now version 3.0 of HMMER which is real nice and should substitute the 2.3 version. Support of MPI is now available, even though this package does not offer it yet. The PVM of version 2.3 is no longer supported by upstream and not shipping any longer with Debian. The packaging is lintian-clean, albeit not perfect. Steffen and Eric at the BOSC Codefest 2010 in Boston. Special thanks go to Gregor for fixing the build on the PowerPC platform. debian/hmmer-doc.docs0000644000000000000000000000003012214301224011673 0ustar Userguide.pdf tutorial/ debian/changelog0000644000000000000000000001431512247133674011055 0ustar hmmer (3.1b1-3) unstable; urgency=low * Apply patch from Adam Conrad to build on powerpc (thanks to Adam for the patch) Closes: #728650 * DEP3 patch headers * cme fix dpkg-control -- Andreas Tille Mon, 02 Dec 2013 17:24:47 +0100 hmmer (3.1b1-2) unstable; urgency=low [ Charles Plessy ] * Removed myself from the Uploaders. [ Andreas Tille ] * debian/rules: Use --with autotools_dev Closes: #727386 -- Andreas Tille Thu, 24 Oct 2013 08:37:52 +0200 hmmer (3.1b1-1) unstable; urgency=low * Upload changes from BioLinux to Debian * debian/control: - cme fix dpkg-control - provide real package (evince) for pdf-viewer - debhelper 9 - anonscm for Vcs fields -- Andreas Tille Thu, 15 Aug 2013 20:20:03 +0200 hmmer (3.1b1-0biolinux1) precise; urgency=low * New upstream * Switch to DH in rules as CDBS does my nut in * Simplify hmmer.install and kill hmmer.manpages * Added binaries: alimask hmmc2 hmmlogo hmmpgmd nhmmer nhmmscan * Modify watchfile to see new version * Avoid compressing all the tutorial data * make distclean was failing :- fixed with patch -- Tim Booth Thu, 15 Aug 2013 16:34:31 +0100 hmmer (3.0-4) unstable; urgency=low [ Charles Plessy ] * renamed debian/upstream-metadata.yaml to debian/upstream [ Andreas Tille ] * debian/upstream: Took over additional citation from tasks file * debian/control: - Standards-Version: 3.9.3 (no changes needed) - Fixed Vcs fields * debhelper 8 (control + compat) * debian/docs: removed because empty * debian/copyright: - Rewritten to match DEP5 (verified using `cme fix dpkg-copyright`) - Added Files: easel:* section * debian/rules: Fixed clean target by cleaning up easel/testsuite dir -- Andreas Tille Tue, 03 Apr 2012 09:53:16 +0200 hmmer (3.0-3) unstable; urgency=low * Fix "FTBFS (powerpc): altivec and cast errors": remove special casing for powerpc, so that it gets built with the dummy vector implementation like most other architectures - contributed by Gregor Herrrmann (Closes: #594860). -- Steffen Moeller Mon, 25 Oct 2010 00:08:19 +0200 hmmer (3.0-2) unstable; urgency=low * Install binaries to /usr/bin instead of /bin * Standards-Version: 3.9.1 (no changes needed) -- Andreas Tille Fri, 27 Aug 2010 07:53:17 +0200 hmmer (3.0-1) unstable; urgency=low * The 3.0 release should now substitute the outdated 2.3.x one. * The hmmer-pvm package is no longer available. -- Eric Talevich Thu, 08 Jul 2010 14:17:59 -0400 hmmer (2.3.2-6) UNRELEASED; urgency=low * 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). * Gathered some metadata about upstream in debian/upstream-metadata.yaml. * Checked conformance with Policy 3.8.3 and incremented Standards-Version in debian/control to reflect it. -- Charles Plessy Wed, 16 Dec 2009 13:21:02 +0900 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 debian/patches/0000755000000000000000000000000012247133555010624 5ustar debian/patches/debian-changes-3.0-2.10000644000000000000000000000155612247133306014174 0ustar Author: gregor herrmann Last-Update: Mon, 25 Oct 2010 00:25:08 +0200 Bug-Debian: http://bugs.debian.org/594860 Description: avoid altivec and cast errors on powerpc I've created a patch the uses "dummy" also on powerpc, and it works on i386 and powerpc (meaning that sse is used on my local machine and dummy on pescetti.debian.org). --- a/configure +++ b/configure @@ -3849,7 +3849,6 @@ ia64-*-*) impl_choice=sse;; i?86-*-*) impl_choice=sse;; x86*-*-*) impl_choice=sse;; - powerpc*-*-*) impl_choice=vmx;; *) impl_choice=dummy;; esac fi --- a/configure.ac +++ b/configure.ac @@ -313,7 +313,6 @@ ia64-*-*) impl_choice=sse;; i?86-*-*) impl_choice=sse;; x86*-*-*) impl_choice=sse;; - powerpc*-*-*) impl_choice=vmx;; *) impl_choice=dummy;; esac fi debian/patches/fix_clean_target0000644000000000000000000000331712247133555014051 0ustar Author: Tim Booth Last-Update: Thu, 15 Aug 2013 16:34:31 +0100 Description: Fix clean target by making sure it will always succeede --- a/documentation/Makefile.in +++ b/documentation/Makefile.in @@ -24,12 +24,12 @@ clean: ${QUIET_SUBDIR0}man ${QUIET_SUBDIR1} clean - ${QUIET_SUBDIR0}userguide ${QUIET_SUBDIR1} clean + ${QUIET_SUBDIR0}userguide ${QUIET_SUBDIR1} clean || true -rm -f *~ distclean: ${QUIET_SUBDIR0}man ${QUIET_SUBDIR1} distclean - ${QUIET_SUBDIR0}userguide ${QUIET_SUBDIR1} distclean + ${QUIET_SUBDIR0}userguide ${QUIET_SUBDIR1} distclean || true -rm -f Makefile ################################################################ @@ -43,4 +43,4 @@ # # SVN $URL: https://svn.janelia.org/eddylab/eddys/src/hmmer/branches/3.1/documentation/Makefile.in $ # SVN $Id: Makefile.in 3649 2011-08-11 15:12:30Z eddys $ -################################################################ \ No newline at end of file +################################################################ --- a/easel/Makefile.in +++ b/easel/Makefile.in @@ -485,7 +485,7 @@ # "make clean" removes almost everything except configuration files # clean: - ${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} clean + ${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} clean || true ${QUIET_SUBDIR0}testsuite ${QUIET_SUBDIR1} clean ${QUIET_SUBDIR0}miniapps ${QUIET_SUBDIR1} clean -rm -f ${OBJS} libeasel.a @@ -502,7 +502,7 @@ distclean: clean - ${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} distclean + ${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} distclean || true ${QUIET_SUBDIR0}testsuite ${QUIET_SUBDIR1} distclean ${QUIET_SUBDIR0}miniapps ${QUIET_SUBDIR1} distclean -rm esl_config.h debian/patches/series0000644000000000000000000000007512203212144012023 0ustar debian-changes-3.0-1 debian-changes-3.0-2.1 fix_clean_target debian/patches/debian-changes-3.0-10000644000000000000000000000047412247133435014035 0ustar Author: Eric Talevich Last-Update: Thu, 08 Jul 2010 14:17:59 -0400 Description: Fix manpage extension --- a/Makefile.in +++ b/Makefile.in @@ -47,7 +47,7 @@ pdfdir = @pdfdir@ mandir = @mandir@ man1dir = ${mandir}/man1 -man1ext = .1 +man1ext = 1 # Compiler configuration # debian/compat0000644000000000000000000000000212214301224010353 0ustar 9