[med-svn] r16023 - in trunk/packages: . idba idba/trunk idba/trunk/debian idba/trunk/debian/source idba/trunk/debian/upstream
Andreas Tille
tille at moszumanska.debian.org
Thu Feb 13 14:34:31 UTC 2014
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 <tille at debian.org> 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 <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+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 <ypeng at cs.hku.hk>
+License: GPLv2+
+
+Files: debian/*
+Copyright: 2014 Andreas Tille <tille at debian.org>
+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)
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