Author: tille Date: 2014-02-13 14:34:31 +0000 (Thu, 13 Feb 2014) New Revision: 16023
Added: trunk/packages/idba/ trunk/packages/idba/trunk/ trunk/packages/idba/trunk/debian/ trunk/packages/idba/trunk/debian/changelog trunk/packages/idba/trunk/debian/compat trunk/packages/idba/trunk/debian/control trunk/packages/idba/trunk/debian/copyright trunk/packages/idba/trunk/debian/createmanpages trunk/packages/idba/trunk/debian/idba_hybrid.1 trunk/packages/idba/trunk/debian/links trunk/packages/idba/trunk/debian/manpages trunk/packages/idba/trunk/debian/rules trunk/packages/idba/trunk/debian/source/ trunk/packages/idba/trunk/debian/source/format trunk/packages/idba/trunk/debian/upstream/ trunk/packages/idba/trunk/debian/upstream/metadata trunk/packages/idba/trunk/debian/watch Log: Inject initial packaging for idba; Note: citation data are in debian/upstream/metadata to have a test case for the patched machine-readable gatherer Added: trunk/packages/idba/trunk/debian/changelog =================================================================== --- trunk/packages/idba/trunk/debian/changelog (rev 0) +++ trunk/packages/idba/trunk/debian/changelog 2014-02-13 14:34:31 UTC (rev 16023) @@ -0,0 +1,5 @@ +idba (1.1.1-1) UNRELEASED; urgency=low + + * Initial release (Closes: #<bug>) + + -- Andreas Tille <[email protected]> Thu, 13 Feb 2014 13:57:55 +0100 Added: trunk/packages/idba/trunk/debian/compat =================================================================== --- trunk/packages/idba/trunk/debian/compat (rev 0) +++ trunk/packages/idba/trunk/debian/compat 2014-02-13 14:34:31 UTC (rev 16023) @@ -0,0 +1 @@ +9 Added: trunk/packages/idba/trunk/debian/control =================================================================== --- trunk/packages/idba/trunk/debian/control (rev 0) +++ trunk/packages/idba/trunk/debian/control 2014-02-13 14:34:31 UTC (rev 16023) @@ -0,0 +1,25 @@ +Source: idba +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Andreas Tille <[email protected]> +Build-Depends: debhelper (>= 9) +Standards-Version: 3.9.5 +Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/idba/trunk/ +Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/idba/trunk/ +Homepage: http://i.cs.hku.hk/~alse/hkubrg/projects/idba_tran/ + +Package: idba +Architecture: any +Depends: ${shlibs:Depends}, + ${misc:Depends}, + python +Description: iterative De Bruijn Graph De Novo short read assembler for transcriptome + IDBA-Tran is an iterative De Bruijn Graph De Novo short read assembler + for transcriptome. It is purely de novo assembler based on only RNA + sequencing reads. IDBA-Tran uses local assembly to reconstructing + missing k-mers in low-expressed transcripts and then employs progressive + cutoff on contigs to separate the graph into components. Each component + corresponds to one gene in most cases and contains not many transcripts. + A heuristic algorithm based on pair-end reads is then used to find the + isoforms. Added: trunk/packages/idba/trunk/debian/copyright =================================================================== --- trunk/packages/idba/trunk/debian/copyright (rev 0) +++ trunk/packages/idba/trunk/debian/copyright 2014-02-13 14:34:31 UTC (rev 16023) @@ -0,0 +1,25 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: IDBA-Tran +Source: https://code.google.com/p/hku-idba/downloads/list + +Files: * +Copyright: 2009-2013 Yu Peng <[email protected]> +License: GPLv2+ + +Files: debian/* +Copyright: 2014 Andreas Tille <[email protected]> +License: GPLv2+ + +License: GPLv2+ + 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 2 + 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. + . + On Debian Systems you can find a copy of the GNU General Public + License version 2 at /usr/share/common-licenses/GPL-2. Added: trunk/packages/idba/trunk/debian/createmanpages =================================================================== --- trunk/packages/idba/trunk/debian/createmanpages (rev 0) +++ trunk/packages/idba/trunk/debian/createmanpages 2014-02-13 14:34:31 UTC (rev 16023) @@ -0,0 +1,7 @@ +#!/bin/sh +VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//'` +MANDIR=debian +mkdir -p $MANDIR +help2man --no-info --no-discard-stderr \ + --name='Iterative de Bruijn Graph Assembler for hybrid sequencing data' \ + --version-string="$VERSION" idba_hybrid > $MANDIR/idba_hybrid.1 Property changes on: trunk/packages/idba/trunk/debian/createmanpages ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/idba/trunk/debian/idba_hybrid.1 =================================================================== --- trunk/packages/idba/trunk/debian/idba_hybrid.1 (rev 0) +++ trunk/packages/idba/trunk/debian/idba_hybrid.1 2014-02-13 14:34:31 UTC (rev 16023) @@ -0,0 +1,101 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.43.3. +.TH IDBA_HYBRID "1" "February 2014" "idba_hybrid 1.1.1" "User Commands" +.SH NAME +idba_hybrid \- Iterative de Bruijn Graph Assembler for hybrid sequencing data +.SH SYNOPSIS +.B idba_hybrid +\fI\-r read.fa \-o output_dir \fR[\fI\-\-reference ref.fa\fR] +.SH DESCRIPTION +IDBA-Tran is an iterative De Bruijn Graph De Novo short read assembler +for transcriptome. It is purely de novo assembler based on only RNA +sequencing reads. IDBA-Tran uses local assembly to reconstructing +missing k-mers in low-expressed transcripts and then employs progressive +cutoff on contigs to separate the graph into components. Each component +corresponds to one gene in most cases and contains not many transcripts. +A heuristic algorithm based on pair-end reads is then used to find the +isoforms. +.SH OPTIONS +.TP +\fB\-o\fR, \fB\-\-out\fR arg (=out) +output directory +.TP +\fB\-r\fR, \fB\-\-read\fR arg +fasta read file (<=128) +.TP +\fB\-\-read_level_2\fR arg +paired\-end reads fasta for second level scaffolds +.TP +\fB\-\-read_level_3\fR arg +paired\-end reads fasta for third level scaffolds +.TP +\fB\-\-read_level_4\fR arg +paired\-end reads fasta for fourth level scaffolds +.TP +\fB\-\-read_level_5\fR arg +paired\-end reads fasta for fifth level scaffolds +.TP +\fB\-l\fR, \fB\-\-long_read\fR arg +fasta long read file (>128) +.TP +\fB\-\-reference\fR arg +reference genome +.TP +\fB\-\-mink\fR arg (=20) +minimum k value (<=124) +.TP +\fB\-\-maxk\fR arg (=100) +maximum k value (<=124) +.TP +\fB\-\-step\fR arg (=20) +increment of k\-mer of each iteration +.TP +\fB\-\-inner_mink\fR arg (=10) +inner minimum k value +.TP +\fB\-\-inner_step\fR arg (=5) +inner increment of k\-mer +.TP +\fB\-\-prefix\fR arg (=3) +prefix length used to build sub k\-mer table +.TP +\fB\-\-min_count\fR arg (=2) +minimum multiplicity for filtering k\-mer when building the graph +.TP +\fB\-\-min_support\fR arg (=1) +minimum supoort in each iteration +.TP +\fB\-\-num_threads\fR arg (=0) +number of threads +.TP +\fB\-\-seed_kmer\fR arg (=30) +seed kmer size for alignment +.TP +\fB\-\-min_contig\fR arg (=200) +minimum size of contig +.TP +\fB\-\-min_region\fR arg (=500) +minimum size of region in reference genome +.TP +\fB\-\-similar\fR arg (=0.95) +similarity for alignment +.TP +\fB\-\-max_mismatch\fR arg (=3) +max mismatch of error correction +.TP +\fB\-\-min_pairs\fR arg (=3) +minimum number of pairs +.TP +\fB\-\-max_gap\fR arg (=50) +maximum gap in reference +.TP +\fB\-\-no_local\fR +do not use local assembly +.TP +\fB\-\-no_coverage\fR +do not iterate on coverage +.TP +\fB\-\-no_correct\fR +do not do correction +.TP +\fB\-\-pre_correction\fR +perform pre\-correction before assembly Added: trunk/packages/idba/trunk/debian/links =================================================================== --- trunk/packages/idba/trunk/debian/links (rev 0) +++ trunk/packages/idba/trunk/debian/links 2014-02-13 14:34:31 UTC (rev 16023) @@ -0,0 +1,2 @@ +usr/bin/idba_hybrid usr/bin/idba +usr/share/man/man1/idba_hybrid.1.gz usr/share/man/man1/idba.1.gz Added: trunk/packages/idba/trunk/debian/manpages =================================================================== --- trunk/packages/idba/trunk/debian/manpages (rev 0) +++ trunk/packages/idba/trunk/debian/manpages 2014-02-13 14:34:31 UTC (rev 16023) @@ -0,0 +1 @@ +debian/*.1 Added: trunk/packages/idba/trunk/debian/rules =================================================================== --- trunk/packages/idba/trunk/debian/rules (rev 0) +++ trunk/packages/idba/trunk/debian/rules 2014-02-13 14:34:31 UTC (rev 16023) @@ -0,0 +1,14 @@ +#!/usr/bin/make -f + +# DH_VERBOSE := 1 + +DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}') + +%: + dh $@ + +override_dh_install: + dh_install + # for the moment the role of these scripts is totally unknown but they do not seem to be necessary + rm -f debian/$(DEBPKGNAME)/usr/bin/*.py + rm -f debian/$(DEBPKGNAME)/usr/bin/validate_blat* Property changes on: trunk/packages/idba/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/idba/trunk/debian/source/format =================================================================== --- trunk/packages/idba/trunk/debian/source/format (rev 0) +++ trunk/packages/idba/trunk/debian/source/format 2014-02-13 14:34:31 UTC (rev 16023) @@ -0,0 +1 @@ +3.0 (quilt) Added: trunk/packages/idba/trunk/debian/upstream/metadata =================================================================== --- trunk/packages/idba/trunk/debian/upstream/metadata (rev 0) +++ trunk/packages/idba/trunk/debian/upstream/metadata 2014-02-13 14:34:31 UTC (rev 16023) @@ -0,0 +1,12 @@ +Reference: + Author: Yu Peng and Henry C. M. Leung and S. M. Yiu and Francis Y. L. Chin + Title: "IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth" + Journal: Bioinformatics + Year: 2012 + Volume: 28 + Number: 11 + Pages: 1420-1428 + DOI: 10.1093/bioinformatics/bts174 + PMID: 22495754 + URL: http://bioinformatics.oxfordjournals.org/content/28/11/1420.full + eprint: http://bioinformatics.oxfordjournals.org/content/28/11/1420.full.pdf+html Added: trunk/packages/idba/trunk/debian/watch =================================================================== --- trunk/packages/idba/trunk/debian/watch (rev 0) +++ trunk/packages/idba/trunk/debian/watch 2014-02-13 14:34:31 UTC (rev 16023) @@ -0,0 +1,2 @@ +version=3 +http://code.google.com/p/hku-idba/downloads/list?can=1 .*/idba-(\d[\d.]*)\.(?:zip|tgz|tbz2|txz|tar\.gz|tar\.bz2|tar\.xz) _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
