--- exonerate-2.2.0.orig/debian/watch +++ exonerate-2.2.0/debian/watch @@ -0,0 +1,3 @@ +version=3 +http://www.ebi.ac.uk/~guy/exonerate/exonerate-([0-9.]*)\.tar\.gz + --- exonerate-2.2.0.orig/debian/copyright +++ exonerate-2.2.0/debian/copyright @@ -0,0 +1,39 @@ +Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=129 +Upstream-Author: 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 +Packaged-By: This package was debianized by Steffen Moeller +Packaged-Date: Mon, 02 Jul 2007 11:42:38 +0200 +Original-Source-Location: 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 +License: GPL-3+ + (see above) --- exonerate-2.2.0.orig/debian/changelog +++ exonerate-2.2.0/debian/changelog @@ -0,0 +1,79 @@ +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 --- exonerate-2.2.0.orig/debian/README.Debian +++ exonerate-2.2.0/debian/README.Debian @@ -0,0 +1,16 @@ +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 --- exonerate-2.2.0.orig/debian/links +++ exonerate-2.2.0/debian/links @@ -0,0 +1,25 @@ +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 + --- exonerate-2.2.0.orig/debian/compat +++ exonerate-2.2.0/debian/compat @@ -0,0 +1 @@ +7 --- exonerate-2.2.0.orig/debian/rules +++ exonerate-2.2.0/debian/rules @@ -0,0 +1,6 @@ +#!/usr/bin/make -f + +include /usr/share/cdbs/1/class/autotools.mk +include /usr/share/cdbs/1/rules/debhelper.mk + +DEB_MAKE_CHECK_TARGET = -C test check --- exonerate-2.2.0.orig/debian/reference +++ exonerate-2.2.0/debian/reference @@ -0,0 +1,13 @@ +@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}, +} --- exonerate-2.2.0.orig/debian/exonerate.manpages +++ exonerate-2.2.0/debian/exonerate.manpages @@ -0,0 +1,2 @@ +doc/man/man1/*.1 +debian/manpages/fastaoverlap.1 --- exonerate-2.2.0.orig/debian/control +++ exonerate-2.2.0/debian/control @@ -0,0 +1,33 @@ +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 (>= 7.1), autotools-dev, libglib2.0-dev, libreadline-dev, cdbs +Standards-Version: 3.8.3 +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/exonerate/trunk/?rev=0&sc=0 +Vcs-Svn: svn://svn.debian.org/svn/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 --- exonerate-2.2.0.orig/debian/docs +++ exonerate-2.2.0/debian/docs @@ -0,0 +1,4 @@ +README +TODO +AUTHORS +ChangeLog --- exonerate-2.2.0.orig/debian/manpages/fastaoverlap.1 +++ exonerate-2.2.0/debian/manpages/fastaoverlap.1 @@ -0,0 +1,122 @@ +.\" 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).