[med-svn] r9172 - in trunk/packages/gassst/trunk: . debian debian/source
olivier sallou
osallou-guest at alioth.debian.org
Wed Jan 4 15:20:59 UTC 2012
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 <olivier.sallou at irisa.fr> 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 <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Olivier Sallou <olivier.sallou at irisa.fr>
+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 <olivier.sallou at irisa.fr>
+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 <Guillaume.Rizk at irisa.fr>
+ 2011, IRISA Dominique Lavanier <Dominique.lavenier at irisa.fr>
+License: CeCILL
+ Notice
+ .
+ This Agreement is a Free Software license agreement that is the result
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+ .
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+ .
+ The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
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+ .
+ Commissariat à l'Energie Atomique - CEA, a public scientific, technical
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+ 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 <dominique.lavanier at irisa.fr>
+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
+
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