Author: osallou
Date: 2013-02-09 10:56:54 +0000 (Sat, 09 Feb 2013)
New Revision: 12964
Added:
trunk/packages/soap/soapdenovo2/trunk/debian/
trunk/packages/soap/soapdenovo2/trunk/debian/README.Debian
trunk/packages/soap/soapdenovo2/trunk/debian/changelog
trunk/packages/soap/soapdenovo2/trunk/debian/compat
trunk/packages/soap/soapdenovo2/trunk/debian/control
trunk/packages/soap/soapdenovo2/trunk/debian/copyright
trunk/packages/soap/soapdenovo2/trunk/debian/docs
trunk/packages/soap/soapdenovo2/trunk/debian/install
trunk/packages/soap/soapdenovo2/trunk/debian/patches/
trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_gcc_path
trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_usage_name
trunk/packages/soap/soapdenovo2/trunk/debian/patches/series
trunk/packages/soap/soapdenovo2/trunk/debian/rules
trunk/packages/soap/soapdenovo2/trunk/debian/soapdenovo2.1
trunk/packages/soap/soapdenovo2/trunk/debian/soapdenovo2.manpages
trunk/packages/soap/soapdenovo2/trunk/debian/source/
trunk/packages/soap/soapdenovo2/trunk/debian/source/format
trunk/packages/soap/soapdenovo2/trunk/debian/upstream
trunk/packages/soap/soapdenovo2/trunk/debian/watch
Log:
[svn-inject] Applying Debian modifications (223-1) to trunk
Property changes on: trunk/packages/soap/soapdenovo2/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/soap/soapdenovo2/trunk/debian/README.Debian
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/README.Debian
(rev 0)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/README.Debian 2013-02-09
10:56:54 UTC (rev 12964)
@@ -0,0 +1,9 @@
+* SOAPdenovo2
+
+Binaries are soapdenovo2-63mer and soapdenovo2-127mer.
+See manpage for further explanations
+
+SparsePregraph does not compile from source, as such binaries are not provided.
+
+ -- Olivier Sallou <[email protected]> Sat, 09 Feb 2013 10:40:45 +0100
+
Added: trunk/packages/soap/soapdenovo2/trunk/debian/changelog
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/changelog
(rev 0)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/changelog 2013-02-09
10:56:54 UTC (rev 12964)
@@ -0,0 +1,5 @@
+soapdenovo2 (223-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #700160)
+
+ -- Olivier Sallou <[email protected]> Sat, 09 Feb 2013 10:40:45 +0100
Added: trunk/packages/soap/soapdenovo2/trunk/debian/compat
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/compat
(rev 0)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/compat 2013-02-09 10:56:54 UTC
(rev 12964)
@@ -0,0 +1 @@
+8
Added: trunk/packages/soap/soapdenovo2/trunk/debian/control
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/control
(rev 0)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/control 2013-02-09
10:56:54 UTC (rev 12964)
@@ -0,0 +1,24 @@
+Source: soapdenovo2
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 8),g++
+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/soap/soapdenovo2/trunk/
+Vcs-Browser:
http://svn.debian.org/wsvn/debian-med/trunk/packages/soap/soapdenovo2/
+Standards-Version: 3.9.3
+Homepage: http://soap.genomics.org.cn/soapdenovo.html
+
+Package: soapdenovo2
+Architecture: any-amd64 any-ppc64 any-ia64
+#Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: short-read assembly method to build de novo draft assembly
+ SOAPdenovo is a novel short-read assembly method that can build a de novo
draft
+ assembly for the human-sized genomes. The program is specially designed to
+ assemble Illumina GA short reads.
+ .
+ It creates new opportunities for building reference
+ sequences and carrying out accurate analyses of unexplored genomes in a cost
+ effective way.
Added: trunk/packages/soap/soapdenovo2/trunk/debian/copyright
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/copyright
(rev 0)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/copyright 2013-02-09
10:56:54 UTC (rev 12964)
@@ -0,0 +1,41 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: soapdenovo
+Source: http://soap.genomics.org.cn/soapdenovo.html
+
+Files: *
+Copyright: 2008-2010 BGI-Shenzhen
+License: GPL-3+
+ This package 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 package 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 <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
+
+Files: debian/*
+Copyright: 2012 Olivier Sallou <[email protected]>
+License: GPL-2+
+ This package 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 package 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 <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
Added: trunk/packages/soap/soapdenovo2/trunk/debian/docs
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/docs
(rev 0)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/docs 2013-02-09 10:56:54 UTC
(rev 12964)
@@ -0,0 +1 @@
+MANUAL
Added: trunk/packages/soap/soapdenovo2/trunk/debian/install
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/install
(rev 0)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/install 2013-02-09
10:56:54 UTC (rev 12964)
@@ -0,0 +1,2 @@
+standardPregraph/SOAPdenovo-63mer usr/bin/
+standardPregraph/SOAPdenovo-127mer usr/bin/
Added: trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_gcc_path
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_gcc_path
(rev 0)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_gcc_path
2013-02-09 10:56:54 UTC (rev 12964)
@@ -0,0 +1,36 @@
+--- a/sparsePregraph/Makefile
++++ b/sparsePregraph/Makefile
+@@ -1,11 +1,11 @@
+-CC= /opt/blc/gcc-4.5.0/bin/gcc #gcc
++CC= gcc #gcc
+ CFLAGS= -O4 -fomit-frame-pointer #-static #-mcrc32 -march=core2
-msse4.1 -msse4.2
+ DFLAGS=
+ OBJS= build_graph.o build_edge.o multi_threads.o \
+ build_preArc.o pregraph_sparse.o io_func.o\
+ global.o convert_soapdenovo.o
+ PROG=
+-INCLUDES= -I./inc
++INCLUDES= -I./inc
+ SUBDIRS= .
+ LIBPATH= -L/usr/lib64
+ LIBS= -pthread -lz -lstdc++ -L./inc
+--- a/standardPregraph/Makefile
++++ b/standardPregraph/Makefile
+@@ -5,7 +5,7 @@
+ #
+ ###################################
+
+-CC= /opt/blc/gcc-4.5.0/bin/gcc #gcc
++CC= gcc #gcc
+ GCCVERSIONMAJOR := $(shell expr `$(CC) -dumpversion | cut -f1 -d.` \>= 4)
+ GCCVERSIONMINOR := $(shell expr `$(CC) -dumpversion | cut -f2 -d.` \>= 4)
+ CFLAGS= -O4 -fomit-frame-pointer #-static #-mcrc32 -march=core2
-msse4.1 -msse4.2
+@@ -78,8 +78,6 @@
+
+ envTest:
+ @test $(BIT_ERR) != 1 || sh -c 'echo "Fatal: 64bit CPU and
Operating System required!";false;'
+- @test $(GCCVERSIONMAJOR) == 1 || sh -c 'echo "GCC version lower
than 4.4.0";false;'
+- @test $(GCCVERSIONMINOR) == 1 || sh -c 'echo "GCC version lower
than 4.4.0";false;'
+
+ SOAPdenovo: envTest $(OBJS)
+ @printf "Linking...
\r"
Added: trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_usage_name
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_usage_name
(rev 0)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_usage_name
2013-02-09 10:56:54 UTC (rev 12964)
@@ -0,0 +1,11 @@
+--- a/standardPregraph/main.c
++++ b/standardPregraph/main.c
+@@ -99,7 +99,7 @@
+
+ static void display_usage ()
+ {
+- fprintf ( stderr, "\nUsage: SOAPdenovo <command> [option]\n" );
++ fprintf ( stderr, "\nUsage: soapdenovo2-63mer/soapdenovo2-127mer
<command> [option]\n" );
+ fprintf ( stderr, " pregraph construct kmer-graph\n" );
+ fprintf ( stderr, " contig eliminate errors and output
contigs\n" );
+ fprintf ( stderr, " map map reads to contigs\n" );
Added: trunk/packages/soap/soapdenovo2/trunk/debian/patches/series
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/patches/series
(rev 0)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/patches/series 2013-02-09
10:56:54 UTC (rev 12964)
@@ -0,0 +1,2 @@
+fix_gcc_path
+fix_usage_name
Added: trunk/packages/soap/soapdenovo2/trunk/debian/rules
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/rules
(rev 0)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/rules 2013-02-09 10:56:54 UTC
(rev 12964)
@@ -0,0 +1,23 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+ dh $@
+
+override_dh_auto_build:
+ cd standardPregraph && make 63mer=1
+ cd standardPregraph && make 127mer=1
+# cd sparsePregraph && make
+ dh_auto_build
+
+override_dh_install:
+ dh_install
+ cd debian/soapdenovo2/usr/bin/;rename 's/SOAPdenovo/soapdenovo2/' SOAP*
+
+override_dh_clean:
+ cd standardPregraph && make 63mer=1 clean && make 127mer=1 clean
+ cd sparsePregraph && make clean
+ dh_clean
Property changes on: trunk/packages/soap/soapdenovo2/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/soap/soapdenovo2/trunk/debian/soapdenovo2.1
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/soapdenovo2.1
(rev 0)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/soapdenovo2.1 2013-02-09
10:56:54 UTC (rev 12964)
@@ -0,0 +1,22 @@
+.TH soapdenovo2 1 "February 09, 2013" "version 2.2.3" "USER COMMANDS"
+.SH NAME
+soapdenovo2 \- Short-read assembly method that can build a de novo draft
assembly
+.SH SYNOPSIS
+.B soapdenovo_63mer soapdenovo_127mer
+
+.SH Introduction
+
+SOAPdenovo is a novel short-read assembly method that can build a de novo
draft assembly for the human-sized genomes. The program is specially designed
to assemble Illumina GA short reads. It creates new opportunities for building
reference sequences and carrying out accurate analyses of unexplored genomes in
a cost effective way.
+
+1) Support large kmer up to 127 to utilize long reads. Three version are
provided.
+ I. The 31mer version support kmer only <=31.
+ II. The 63mer version support kmer only <=63 and doubles the memory
consumption than 31mer version, even being used with kmer <=31.
+ III. The 127mer version support kmer only <=127 and double the memory
consumption than 63mer version, even being used with kmer <=63.
+
+Please notice that, with longer kmer, the quantity of nodes would decrease
significantly, thus the memory consumption is usually smaller than double with
shifted version.
+
+For more information, look at the MANUAL in /usr/share/doc/soapdenovo2 or on
soapdenovo web site.
+
+.SH AUTHOR
+Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging
+
Added: trunk/packages/soap/soapdenovo2/trunk/debian/soapdenovo2.manpages
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/soapdenovo2.manpages
(rev 0)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/soapdenovo2.manpages
2013-02-09 10:56:54 UTC (rev 12964)
@@ -0,0 +1 @@
+debian/soapdenovo2.1
Added: trunk/packages/soap/soapdenovo2/trunk/debian/source/format
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/source/format
(rev 0)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/source/format 2013-02-09
10:56:54 UTC (rev 12964)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/soap/soapdenovo2/trunk/debian/upstream
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/upstream
(rev 0)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/upstream 2013-02-09
10:56:54 UTC (rev 12964)
@@ -0,0 +1,12 @@
+Name: SOAPdenovo2
+Homepage: http://soap.genomics.org.cn/soapdenovo.html
+Reference:
+ Author: Ruibang Luo1, Binghang Liu1, Yinlong Xie1, Zhenyu Li1, Weihua Huang,
Jianying Yuan, Guangzhu He, Yanxiang Chen, Qi Pan, Yunjie Liu, Jingbo Tang,
Gengxiong Wu, Hao Zhang, Yujian Shi, Yong Liu, Chang Yu, Bo Wang, Yao Lu,
Changlei Han, David W Cheung, Siu-Ming Yiu, Shaoliang Peng, Zhu Xiaoqian,
Guangming Liu, Xiangke Liao, Yingrui Li, Huanming Yang, Jian Wang, Tak-Wah Lam
and Jun Wang
+ Title: SOAPdenovo2: an empirically improved memory-efficient short-read de
novo assembler
+ Journal: Giga Science
+ Year: 2012
+ Volume: 1
+ Number: 1
+ Pages: 18
+ DOI: 10.1186/2047-217X-1-18
+ URL: http://www.gigasciencejournal.com/content/1/1/18
Added: trunk/packages/soap/soapdenovo2/trunk/debian/watch
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/watch
(rev 0)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/watch 2013-02-09 10:56:54 UTC
(rev 12964)
@@ -0,0 +1,5 @@
+# Compulsory line, this is a version 3 file
+version=3
+http://qa.debian.org/watch/sf.php/soapdenovo2/SOAPdenovo2-src-r(.+)\.(?:zip|tgz|tbz2|txz|tar\.gz|tar\.bz2|tar\.xz)
+#http://sf.net/SOAPdenovo2/SOAPdenovo2-src-r(.+)\.(?:zip|tgz|tbz2|txz|tar\.gz|tar\.bz2|tar\.xz)
+#opts=filenamemangle=s/down\/SOAPdenovo-V/soapdenovo-/
http://sourceforge.net/projects/soapdenovo2/files/SOAPdenovo2/
down/SOAPdenovo-V(.*)\.src\.tgz
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