debian/0000755000000000000000000000000011703535317007173 5ustar debian/source/0000755000000000000000000000000011671367711010500 5ustar debian/source/format0000644000000000000000000000001411660156110011671 0ustar 3.0 (quilt) debian/docs0000644000000000000000000000002411671400220010026 0ustar README TODO AUTHORS debian/copyright0000644000000000000000000000324111671370364011131 0ustar Format: http://dep.debian.net/deps/dep5/ Upstream-Contact: Guy St.C. Slater The following have contributed code to this project: (in chronological order) Ewan Birney Ian Holmes Steve Searle Tim Cutts Don Gilbert Michael Schuster Source: http://www.ebi.ac.uk/~guy/exonerate/exonerate-2.0.0.tar.gz Files: * Copyright: © 2000-2008 Guy St.C. Slater License: GPL-3+ This program 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 3 of the License, or (at your option) any later version. . This program 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 program. If not, see . X-Comment: On Debian GNU/Linux systems, the complete text of the GNU General Public License can be found in `/usr/share/common-licenses/GPL' Files: debian/* Copyright: © 2007 Steffen Moeller © 2008 Charles Plessy © 2011 Andreas Tille License: GPL-3+ (see above) debian/compat0000644000000000000000000000000211671367772010405 0ustar 8 debian/upstream-metadata.yaml0000644000000000000000000000075311326521306013474 0ustar Contact: Guy St.C. Slater DOI: 10.1186/1471-2105-6-31 Name: Exonerate Homepage: http://www.ebi.ac.uk/~guy/exonerate/ PMID: 15713233 Reference: Author: Slater, Guy and Birney, Ewan Title: Automated generation of heuristics for biological sequence comparison Journal: BMC Bioinformatics Volume: 6 Year: 2005 Number: 1 Pages: 31 URL: http://www.biomedcentral.com/1471-2105/6/31 ISSN: 1471-2105 Watch: http://www.ebi.ac.uk/~guy/exonerate/exonerate-([0-9.]*)\.tar\.gz debian/control0000644000000000000000000000272411703530522010574 0ustar Source: exonerate Section: science Priority: optional Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes Uploaders: Steffen Moeller , Charles Plessy , Andreas Tille Build-Depends: debhelper (>= 8), autotools-dev, libglib2.0-dev, libreadline-dev, dh-autoreconf Standards-Version: 3.9.2 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/exonerate/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/exonerate/trunk/ Homepage: http://www.ebi.ac.uk/~guy/exonerate/ Package: exonerate Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: wise Enhances: bioperl-run Description: generic tool for pairwise sequence comparison Exonerate allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics. Much of the functionality of the Wise dynamic programming suite was reimplemented in C for better efficiency. Exonerate is an intrinsic component of the building of the Ensembl genome databases, providing similarity scores between RNA and DNA sequences and thus determining splice variants and coding sequences in general. . An In-silico PCR Experiment Simulation System (see the ipcress man page) is packaged with exonerate. . This package also comes with a selection of utilities for performing simple manipulations quickly on fasta files beyond 2Gb debian/links0000644000000000000000000000336211110210537010224 0ustar usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/exonerate-client.1.gz usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/exonerate-server.1.gz usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fasta2esd.1.gz usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastaannotatecdna.1.gz usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastachecksum.1.gz usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastaclean.1.gz usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastaclip.1.gz usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastacomposition.1.gz usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastadiff.1.gz usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastaexplode.1.gz usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastafetch.1.gz usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastahardmask.1.gz usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastaindex.1.gz usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastalength.1.gz usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastanrdb.1.gz usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastareformat.1.gz usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastaremove.1.gz usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastarevcomp.1.gz usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastasoftmask.1.gz usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastasort.1.gz usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastasplit.1.gz usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastasubseq.1.gz usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastatranslate.1.gz usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastavalidcds.1.gz debian/exonerate.manpages0000644000000000000000000000006011110210537012660 0ustar doc/man/man1/*.1 debian/manpages/fastaoverlap.1 debian/patches/0000755000000000000000000000000011703532567010626 5ustar debian/patches/manpages.patch0000644000000000000000000000230711671402131013427 0ustar Author: Andreas Tille Date: Mon, 12 Dec 2011 13:13:02 +0100 Description: Fix some errors in manpages. More errors can be found using LC_ALL=en_US.UTF-8 MANWIDTH=80 man --warnings -E UTF-8 -l >/dev/null --- exonerate-2.2.0.orig/doc/man/man1/exonerate.1 +++ exonerate-2.2.0/doc/man/man1/exonerate.1 @@ -33,7 +33,6 @@ .RE .SH CONVENTIONS -.T A number of conventions (and idiosyncracies) are used within exonerate. An understanding of them facilitates interpretation of the output. --- exonerate-2.2.0.orig/doc/man/man1/exonerate-server.1 +++ exonerate-2.2.0/doc/man/man1/exonerate-server.1 @@ -19,7 +19,6 @@ .RE .SH OVERVIEW -.T .\" Firstly, an .B .esd --- exonerate-2.2.0.orig/doc/man/man1/fastautils.1 +++ exonerate-2.2.0/doc/man/man1/fastautils.1 @@ -55,9 +55,6 @@ databases which are distributed with the exonerate sequence alignment program. .P -.\" -... -.\" .RE .\" .SH ENVIRONMENT --- exonerate-2.2.0.orig/doc/man/man1/ipcress.1 +++ exonerate-2.2.0/doc/man/man1/ipcress.1 @@ -35,7 +35,6 @@ .\" .RE .SH INPUT FORMAT -.T The input for ipcress is a simple white-space delimited file describing one experiment per line. Each line contains the following 5 fields: debian/patches/series0000644000000000000000000000005111703532567012037 0ustar fix_build-as-needed.patch manpages.patch debian/patches/fix_build-as-needed.patch0000644000000000000000000000065511671370774015451 0ustar Author: Micah Gersten Date: Mon, 12 Dec 2011 09:15:02 UTC Closes: #651802 --- exonerate-2.2.0.orig/configure.in +++ exonerate-2.2.0/configure.in @@ -289,7 +289,7 @@ if test "$enable_pthreads" = yes; then echo "Using PTHREADS" CFLAGS="$CFLAGS -DUSE_PTHREADS" - LDFLAGS="$LDFLAGS -lpthread" + LIBS="$LIBS -lpthread" elif test "$enable_pthreads" = no; then echo "Not using pthreads" else debian/README.Debian0000644000000000000000000000105011110210537011212 0ustar exonerate for Debian -------------------- Charles has fixed the man pages for this package - many thanks to him. The upstream author, Guy Slater, is very supportive of Debian. He even gave brief instructions on how to build a package in his README. This is much appreciated. Guy was contacted asking for a clarification of the version of the GPL he refers to and to avoid the web link in the C sources to a (now) later version than he distributes with the source. Steffen -- Steffen Moeller Mon, 02 Jul 2007 11:42:38 +0200 debian/manpages/0000755000000000000000000000000011671367500010767 5ustar debian/manpages/fastaoverlap.10000644000000000000000000000470311671367500013544 0ustar .\" Hey, EMACS: -*- nroff -*- .\" First parameter, NAME, should be all caps .\" Second parameter, SECTION, should be 1-8, maybe w/ subsection .\" other parameters are allowed: see man(7), man(1) .TH EXONERATE 1 "30 Jun 2007" .\" Please adjust this date whenever revising the manpage. .\" .\" Some roff macros, for reference: .\" .nh disable hyphenation .\" .hy enable hyphenation .\" .ad l left justify .\" .ad b justify to both left and right margins .\" .nf disable filling .\" .fi enable filling .\" .br insert line break .\" .sp insert n+1 empty lines .\" for manpage-specific macros, see man(7) .SH NAME exonerate \- suite for investigating DNA and RNA sequence similarities .SH SYNOPSIS .B exonerate-client .RI [ --help ] .br .B exonerate-server .RI [ --help ] .br .B fasta2esd .RI [ --help ] .br .B fastaannotatecdna .RI [ --help ] .br .B fastachecksum .RI [ --help ] .br .B fastaclean .RI [ --help ] .br .B fastaclip .RI [ --help ] .br .B fastacomposition .RI [ --help ] .br .B fastadiff .RI [ --help ] .br .B fastaexplode .RI [ --help ] .br .B fastafetch .RI [ --help ] .br .B fastahardmask .RI [ --help ] .br .B fastaindex .RI [ --help ] .br .B fastalength .RI [ --help ] .br .B fastanrdb .RI [ --help ] .br .B fastaoverlap .RI [ --help ] .br .B fastareformat .RI [ --help ] .br .B fastaremove .RI [ --help ] .br .B fastarevcomp .RI [ --help ] .br .B fastasoftmask .RI [ --help ] .br .B fastasort .RI [ --help ] .br .B fastasplit .RI [ --help ] .br .B fastasubseq .RI [ --help ] .br .B fastatranslate .RI [ --help ] .br .B fastavalidcds .RI [ --help ] .br .SH DESCRIPTION These programs are not described by the upstream author, however, some information is available via the --help and -h arguments for all these programs. Whoever is using any of these programs in routine, is requested to provide a seed of a respective man page to the upstream author. .PP .SH OPTIONS .TP .B \-h, .B \-\-help Show summary of options. .TP .B \-v, \-\-version Show version of program. .SH SEE ALSO .BR http://www.ebi.ac.uk/~guy/exonerate/ .br The author of this package provides a beginner ( .IR http://www.ebi.ac.uk/~guy/exonerate/beginner.html ) and and avanced .RI http://www.ebi.ac.uk/~guy/exonerate/advanced.html ) tutorial on his web pages. .SH AUTHOR exonerate was written by Guy Slater . .PP This manual page was written by Steffen Moeller for the Debian project (but may be used by others). debian/reference0000644000000000000000000000056611241261500011046 0ustar @Article{15713233, AUTHOR = { Slater, Guy and Birney, Ewan}, TITLE = {Automated generation of heuristics for biological sequence comparison}, JOURNAL = {BMC Bioinformatics}, VOLUME = {6}, YEAR = {2005}, NUMBER = {1}, PAGES = {31}, URL = {http://www.biomedcentral.com/1471-2105/6/31}, DOI = {10.1186/1471-2105-6-31}, PubMedID = {15713233}, ISSN = {1471-2105}, } debian/watch0000644000000000000000000000011411110210537010202 0ustar version=3 http://www.ebi.ac.uk/~guy/exonerate/exonerate-([0-9.]*)\.tar\.gz debian/changelog0000644000000000000000000001056011703533052011041 0ustar exonerate (2.2.0-6) unstable; urgency=low * debian/patches/autoreconf.patch: Removed because not needed when using dh-autoreconf -- Andreas Tille Thu, 12 Jan 2012 11:29:32 +0100 exonerate (2.2.0-5) unstable; urgency=low * Rather use dh-autoreconf as advised in another patch from Micah Gersten (thanks for your patience) Finally Closes #651802 -- Andreas Tille Thu, 12 Jan 2012 11:11:06 +0100 exonerate (2.2.0-4) unstable; urgency=low * Use autotools_dev properly Closes: #651802 -- Andreas Tille Fri, 06 Jan 2012 23:04:31 +0100 exonerate (2.2.0-3) unstable; urgency=low [ Charles Plessy ] * Documented some meta-information in ‘debian/upstream-metadata.yaml’. [ Andreas Tille ] * debian/source/format: 3.0 (quilt) * debian/control: - Standards-Version: 3.9.2 (no changes needed) - Fixed Vcs fields * Debhlper 8 (control+compat) * debian/copyright: some DEP5 changes * debian/patches/fix_build-as-needed.patch: Fix build with --as-needed (Thanks to Micah Gersten ) Closes: #651802 * debian/patches/autoreconf.patch: Build with recent autotools * debian/patches/manpages.patch: Fix some lintian warnings * debian/rules: - Convert to short dh notation - Remove codegen in clean target - Install upstream changelog only once -- Andreas Tille Mon, 12 Dec 2011 13:13:02 +0100 exonerate (2.2.0-2) unstable; urgency=low [ Charles Plessy ] * debian/control: - Enhances bioperl-run instead of bioperl. - Incremented Standards-Version to reflect conformance with Policy 3.8.3 (no changes needed). [ Andreas Tille ] * debian/control - s/libreadline5-dev/libreadline-dev/ - s/Debian-Med/Debian Med/ -- Andreas Tille Sun, 13 Sep 2009 17:34:07 +0200 exonerate (2.2.0-1) unstable; urgency=low * New upstream release (LP: #285237). This version includes fixes for problems with excessive memory consumption when compiled against glib-2, and fixes a bug with using exonerate-server with unmasked sequences. -- Charles Plessy Mon, 20 Oct 2008 14:18:36 +0200 exonerate (2.1.0-1) unstable; urgency=low * New upstream release (LP: #254115). - This version includes many optimisations and bug fixes for the exonerate-server. It is now possible to search a whole human-sized genome with a typical cDNA or protein query in under a second. - Exonerate-server uses use pthreads by default. * debian/control, debian/compat: switched to debhelper 7. * debian/control: - Checked conformance with Policy 3.8.0. - Enhances: bioperl. * debian/rules: - `--enable-glib2' removed as now default. - Activated tests after build. * Updated debian/copyright. -- Charles Plessy Mon, 04 Aug 2008 19:13:05 +0900 exonerate (2.0.0-1) unstable; urgency=low [ David Paleino ] * Updated to Standards-Version 3.8.0 (no changes needed) [ Charles Plessy ] * New upstream release (Closes: #479323) Quoting the upstream changelog: o Modified exonerate to work in Client:Server mode o Fixed --refine to work with SDP alignments o Disabled codegen warnings from bootstrapper during compilation o Added --geneticcode option for using alternative genetic codes o Added --splice5 and --splice3 to allow alternative splice site PSSMs o Fixed several bugs when scanning query sequences (eg. --forcescan query) o Fixed to report query on forward strand whenever possible. o Fixed --ryo sequence dumping with --bestn o Fixed a bug with missing seeds when using --annotation o Changed license to GPLv3 o Added protein2dna:bestfit and protein2genome:bestfit models (works with exhaustive alignment only) * Updated my email address. * debian/control: - Building on glib-2.0 instead of 1.2. - Added a build dependency on libreadline5-dev. - Augmented the long description and changed the short. - Added a build dependency on CDBS. * debian/copyright made machine-readable. * debian/rules switched to cdbs. * debian/dirs: removed. -- Charles Plessy Wed, 02 Jul 2008 11:24:48 +0900 exonerate (1.4.0-1) unstable; urgency=low * Initial release (Closes: #431404). -- Steffen Moeller Mon, 02 Jul 2007 11:42:38 +0200 debian/rules0000755000000000000000000000055411703530607010254 0ustar #!/usr/bin/make -f # -*- makefile -*- # debian/rules file for exonerate # Andreas Tille # GPL %: dh $@ --with autoreconf override_dh_autoreconf: dh_autoreconf --as-needed override_dh_auto_clean: dh_auto_clean rm -rf codegen override_dh_auto_test: $(MAKE) -C test check override_dh_installchangelogs: dh_installchangelogs -k ChangeLog