Author: osallou-guest Date: 2012-01-04 15:20:59 +0000 (Wed, 04 Jan 2012) New Revision: 9172
Added: trunk/packages/gassst/trunk/debian/ trunk/packages/gassst/trunk/debian/changelog trunk/packages/gassst/trunk/debian/compat trunk/packages/gassst/trunk/debian/control trunk/packages/gassst/trunk/debian/copyright trunk/packages/gassst/trunk/debian/dirs trunk/packages/gassst/trunk/debian/docs trunk/packages/gassst/trunk/debian/gassst.1 trunk/packages/gassst/trunk/debian/gassst.install trunk/packages/gassst/trunk/debian/gassst.manpages trunk/packages/gassst/trunk/debian/gassst_to_sam.1 trunk/packages/gassst/trunk/debian/rules trunk/packages/gassst/trunk/debian/source/ trunk/packages/gassst/trunk/debian/source/format trunk/packages/gassst/trunk/debian/upstream-metadata.yaml trunk/packages/gassst/trunk/debian/watch Log: [svn-inject] Applying Debian modifications (1.28-1) to trunk Property changes on: trunk/packages/gassst/trunk/debian ___________________________________________________________________ Added: mergeWithUpstream + 1 Added: trunk/packages/gassst/trunk/debian/changelog =================================================================== --- trunk/packages/gassst/trunk/debian/changelog (rev 0) +++ trunk/packages/gassst/trunk/debian/changelog 2012-01-04 15:20:59 UTC (rev 9172) @@ -0,0 +1,5 @@ +gassst (1.28-1) UNRELEASED; urgency=low + + * Initial release (Closes: #654603) + + -- Olivier Sallou <[email protected]> Wed, 04 Jan 2012 14:57:27 +0100 Added: trunk/packages/gassst/trunk/debian/compat =================================================================== --- trunk/packages/gassst/trunk/debian/compat (rev 0) +++ trunk/packages/gassst/trunk/debian/compat 2012-01-04 15:20:59 UTC (rev 9172) @@ -0,0 +1 @@ +8 Added: trunk/packages/gassst/trunk/debian/control =================================================================== --- trunk/packages/gassst/trunk/debian/control (rev 0) +++ trunk/packages/gassst/trunk/debian/control 2012-01-04 15:20:59 UTC (rev 9172) @@ -0,0 +1,19 @@ +Source: gassst +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Olivier Sallou <[email protected]> +DM-Upload-Allowed: yes +Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/gassst/trunk/ +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/gassst/trunk/ +Build-Depends: debhelper (>= 8.0.0) +Standards-Version: 3.9.2 +Homepage: http://www.irisa.fr/symbiose/projects/gassst/ + +Package: gassst +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: Global alignment short sequence search tool + GASSST finds global alignments of short DNA sequences against large DNA banks. + Its strong point is its ability to perform fast gapped alignments. + The program takes as inputs banks in FASTA format and finds best alignment. Added: trunk/packages/gassst/trunk/debian/copyright =================================================================== --- trunk/packages/gassst/trunk/debian/copyright (rev 0) +++ trunk/packages/gassst/trunk/debian/copyright 2012-01-04 15:20:59 UTC (rev 9172) @@ -0,0 +1,518 @@ +Format: http://anonscm.debian.org/viewvc/dep/web/deps/dep5.mdwn?revision=174 +Upstream-Name: GASSST +Source: http://www.irisa.fr/symbiose/projects/gassst/ + +Files: debian/* +Copyright: 2011 Olivier Sallou <[email protected]> +License: GPL-3 + On Debian systems, the full text of the GNU General Public + License version 3 can be found in the file + `/usr/share/common-licenses/GPL-3'. + +Files: * +Copyright: 2011, IRISA Guillaume Rizk <[email protected]> + 2011, IRISA Dominique Lavanier <[email protected]> +License: CeCILL + Notice + . + This Agreement is a Free Software license agreement that is the result + of discussions between its authors in order to ensure compliance with + the two main principles guiding its drafting: + . + * firstly, compliance with the principles governing the distribution + of Free Software: access to source code, broad rights granted to + users, + * secondly, the election of a governing law, French law, with which + it is conformant, both as regards the law of torts and + intellectual property law, and the protection that it offers to + both authors and holders of the economic rights over software. + . + The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre]) + license are: + . + Commissariat à l'Energie Atomique - CEA, a public scientific, technical + and industrial research establishment, having its principal place of + business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France. + . + Centre National de la Recherche Scientifique - CNRS, a public scientific + and technological establishment, having its principal place of business + at 3 rue Michel-Ange, 75794 Paris cedex 16, France. + . + Institut National de Recherche en Informatique et en Automatique - + INRIA, a public scientific and technological establishment, having its + principal place of business at Domaine de Voluceau, Rocquencourt, BP + 105, 78153 Le Chesnay cedex, France. + . + . + Preamble + . + The purpose of this Free Software license agreement is to grant users + the right to modify and redistribute the software governed by this + license within the framework of an open source distribution model. + . + The exercising of these rights is conditional upon certain obligations + for users so as to preserve this status for all subsequent redistributions. + . + In consideration of access to the source code and the rights to copy, + modify and redistribute granted by the license, users are provided only + with a limited warranty and the software's author, the holder of the + economic rights, and the successive licensors only have limited liability. + . + In this respect, the risks associated with loading, using, modifying + and/or developing or reproducing the software by the user are brought to + the user's attention, given its Free Software status, which may make it + complicated to use, with the result that its use is reserved for + developers and experienced professionals having in-depth computer + knowledge. 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These subsequent versions may + address new issues encountered by Free Software. + . + 12.3 Any Software distributed under a given version of the Agreement may + only be subsequently distributed under the same version of the Agreement + or a subsequent version, subject to the provisions of Article 5.3.4. + . + . + Article 13 - GOVERNING LAW AND JURISDICTION + . + 13.1 The Agreement is governed by French law. The Parties agree to + endeavor to seek an amicable solution to any disagreements or disputes + that may arise during the performance of the Agreement. + . + 13.2 Failing an amicable solution within two (2) months as from their + occurrence, and unless emergency proceedings are necessary, the + disagreements or disputes shall be referred to the Paris Courts having + jurisdiction, by the more diligent Party. + . + . + Version 2.0 dated 2006-09-05. + Added: trunk/packages/gassst/trunk/debian/dirs =================================================================== --- trunk/packages/gassst/trunk/debian/dirs (rev 0) +++ trunk/packages/gassst/trunk/debian/dirs 2012-01-04 15:20:59 UTC (rev 9172) @@ -0,0 +1 @@ +usr/bin Added: trunk/packages/gassst/trunk/debian/docs =================================================================== --- trunk/packages/gassst/trunk/debian/docs (rev 0) +++ trunk/packages/gassst/trunk/debian/docs 2012-01-04 15:20:59 UTC (rev 9172) @@ -0,0 +1 @@ +README Added: trunk/packages/gassst/trunk/debian/gassst.1 =================================================================== --- trunk/packages/gassst/trunk/debian/gassst.1 (rev 0) +++ trunk/packages/gassst/trunk/debian/gassst.1 2012-01-04 15:20:59 UTC (rev 9172) @@ -0,0 +1,77 @@ +.TH gassst 1 "January 4, 2012" "version 1.28" "USER COMMANDS" +.SH NAME +gassst \- Global Alignment Short Sequence Search Tool +.SH SYNOPSIS +.B gassst -d <bank_file> -i <query_file> -o <output_file> -p <identity_percentage> [options] + +.I [-w <size_seed>] [-m <output_format>] [-l <complexity_filter>] [-t <size_partition>] [-r <reverse_complement>] [-g <gaps_number>] [-n <thread_number>] [-h <max_hits_per_read>] [-s <sensitivity level>] [-b <output best alignments>] [-z <obscure option : bitstat>] +.SH DESCRIPTION +GASSST finds global alignments of short DNA sequences against large DNA banks. + +The program takes as inputs 2 banks in FASTA format: + +- bank_file: a collection of DNA sequences of any length (from short EST sequence to full genome) + +- query file: a collection of very short DNA sequences + +.PP +.SH MANDATORY OPTIONS +.TP +\-d <bank_file> +(string) Name of a DNA sequence bank in FASTA format +.TP +\-i <query_file> +(string) Name of a DNA sequence bank in FASTA format - Short sequences +.TP +\-o <output_file> +(string) Name of the output file to store the results +.TP +\-p <identity_percentage> +(integer) Minimum percentage of identity. Must be in the interval [0 100] +.SH ADDITIONAL OPTIONS +.TP +\-w <size_seed> +(integer) Size of the anchoring seed. Must be in the interval [6 20] (Default : automatic) +.TP +\-m <output_format> +(integer) 1 = standard Gassst format. 0 = human readable format. 8 = blast-like m8 format (Default : 1) +.TP +\-n <thread number> +(integer) Number of processor threads (Default : 1) +.TP +\-l <complexity_filter> +(integer) 0 = low complexity filter off. 1 = low complexity filter on (Default : on) +.TP +\-t <size_partition> +(integer) Maximum size for the bank's partitions in Megabytes. Must be in the interval [1;1 600] (Default : 2% of the RAM size, recommended) +.TP +\-r <reverse_complement> +(integer) 0 = Disable the revert complement research, 1 = Enable the revert complement research (Default : 1) +.TP +\-g <gaps_number> +(integer) Number of gaps allowed. (Default : maximum allowed by identity percentage) +.TP +\-h <max alignment per read> +(integer) Maximum number of alignment per query. 0 means no limit (Default : 100) +.TP +\-s <sensitivity level> +(integer) Sensitivity level, in [0-5]. 0 is fastest, 5 is best sensitivity (Default : 2) +.TP +\-b <output best alignments> +(integer) 1 = output best alignments. 0 = output random alignments, slightly faster (Default : 1) +.SH USAGE +Tool usage is available in /usr/share/doc/gassst/README. +.PP +.SH EXAMPLE +gassst \-d genome.fasta \-i reads.fasta \-o output \-p 90 +.SH SAM CONVERSION +gassst_to_sam output output.sam +.SH CITING +GASSST: global alignment short sequence search tool, Guillaume Rizk,Dominique Lavanier, +Bioinformatics (2010) 26 (20): 2534-2540 doi: 10.1093/bioinformatics/btq485 +.PP +.SH AUTHOR +Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging +Guillaume Rizk,Dominique Lavanier - gassst + + Added: trunk/packages/gassst/trunk/debian/gassst.install =================================================================== --- trunk/packages/gassst/trunk/debian/gassst.install (rev 0) +++ trunk/packages/gassst/trunk/debian/gassst.install 2012-01-04 15:20:59 UTC (rev 9172) @@ -0,0 +1,2 @@ +gassst usr/bin +gassst_to_sam usr/bin Added: trunk/packages/gassst/trunk/debian/gassst.manpages =================================================================== --- trunk/packages/gassst/trunk/debian/gassst.manpages (rev 0) +++ trunk/packages/gassst/trunk/debian/gassst.manpages 2012-01-04 15:20:59 UTC (rev 9172) @@ -0,0 +1,2 @@ +debian/gassst.1 +debian/gassst_to_sam.1 Added: trunk/packages/gassst/trunk/debian/gassst_to_sam.1 =================================================================== --- trunk/packages/gassst/trunk/debian/gassst_to_sam.1 (rev 0) +++ trunk/packages/gassst/trunk/debian/gassst_to_sam.1 2012-01-04 15:20:59 UTC (rev 9172) @@ -0,0 +1,18 @@ +.TH gassst_to_sam 1 "January 4, 2012" "version 1.28" "USER COMMANDS" +.SH NAME +gassst_to_sam \- Convert gassst output to SAM format +.SH SYNOPSIS +.B gassst_to_sam <gassst_outputfile> <output_file.sam> +.SH WARNING +The gassst_to_sam utility currently only takes as input the standard Gassst +output format ("1"), not format "0" or "8". +.PP +.SH CITING +GASSST: global alignment short sequence search tool, Guillaume Rizk,Dominique Lavanier, +Bioinformatics (2010) 26 (20): 2534-2540 doi: 10.1093/bioinformatics/btq485 +.PP +.SH AUTHOR +Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging +Guillaume Rizk,Dominique Lavanier - gassst + + Added: trunk/packages/gassst/trunk/debian/rules =================================================================== --- trunk/packages/gassst/trunk/debian/rules (rev 0) +++ trunk/packages/gassst/trunk/debian/rules 2012-01-04 15:20:59 UTC (rev 9172) @@ -0,0 +1,17 @@ +#!/usr/bin/make -f +# -*- makefile -*- + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +%: + dh $@ + +override_dh_install: + mv Gassst gassst + dh_install + +override_dh_clean: + dh_clean + rm -f gassst + rm -f gassst_to_sam Property changes on: trunk/packages/gassst/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/gassst/trunk/debian/source/format =================================================================== --- trunk/packages/gassst/trunk/debian/source/format (rev 0) +++ trunk/packages/gassst/trunk/debian/source/format 2012-01-04 15:20:59 UTC (rev 9172) @@ -0,0 +1 @@ +3.0 (quilt) Added: trunk/packages/gassst/trunk/debian/upstream-metadata.yaml =================================================================== --- trunk/packages/gassst/trunk/debian/upstream-metadata.yaml (rev 0) +++ trunk/packages/gassst/trunk/debian/upstream-metadata.yaml 2012-01-04 15:20:59 UTC (rev 9172) @@ -0,0 +1,12 @@ +Contact: Dominique Lavanier <[email protected]> +DOI: 10.1093/bioinformatics/btq485 +Homepage: http://www.irisa.fr/symbiose/projects/gassst/ +Name: GASSST +Reference: + author: Guillaume Rizk and Dominique Lavanier + title: GASSST: global alignment short sequence search tool + journal: Bioinformatics + volume: 20 + number: 36 + year: 2010 + URL: http://bioinformatics.oxfordjournals.org/content/26/20/2534.abstract?keytype=ref&ijkey=f5zH80QsuCqixRH Added: trunk/packages/gassst/trunk/debian/watch =================================================================== --- trunk/packages/gassst/trunk/debian/watch (rev 0) +++ trunk/packages/gassst/trunk/debian/watch 2012-01-04 15:20:59 UTC (rev 9172) @@ -0,0 +1,7 @@ +# Compulsory line, this is a version 3 file +version=3 + +# Uncomment to examine a Webpage +# <Webpage URL> <string match> +http://www.irisa.fr/symbiose/projects/gassst/ Gassst_v(.*)\.tar\.gz + _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
