[med-svn] [soapdenovo2] 02/09: Imported Debian patch 223-2
Sascha Steinbiss
sascha at steinbiss.name
Fri May 27 22:37:07 UTC 2016
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository soapdenovo2.
commit d05f5be664489b9f52c34c686a1db30f9d7a0a03
Author: Olivier Sallou <osallou at debian.org>
Date: Sat Feb 9 13:02:55 2013 +0100
Imported Debian patch 223-2
---
debian/README.Debian | 9 +++++
debian/changelog | 11 ++++++
debian/compat | 1 +
debian/control | 24 +++++++++++++
debian/copyright | 84 +++++++++++++++++++++++++++++++++++++++++++
debian/docs | 1 +
debian/install | 2 ++
debian/patches/add_hardening | 30 ++++++++++++++++
debian/patches/fix_gcc_path | 41 +++++++++++++++++++++
debian/patches/fix_usage_name | 18 ++++++++++
debian/patches/series | 3 ++
debian/rules | 34 ++++++++++++++++++
debian/soapdenovo2.1 | 22 ++++++++++++
debian/soapdenovo2.manpages | 1 +
debian/source/format | 1 +
debian/upstream | 12 +++++++
debian/watch | 5 +++
17 files changed, 299 insertions(+)
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..230c5f1
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,9 @@
+* SOAPdenovo2
+
+Binaries are soapdenovo2-63mer and soapdenovo2-127mer.
+See manpage soapdenovo2 for further explanations
+
+SparsePregraph does not compile from source, as such binaries are not provided.
+
+ -- Olivier Sallou <osallou at debian.org> Sat, 09 Feb 2013 10:40:45 +0100
+
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..402464d
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,11 @@
+soapdenovo2 (223-2) unstable; urgency=low
+
+ * debian/copyright: Update copyright years and content
+
+ -- Olivier Sallou <osallou at debian.org> Sat, 09 Feb 2013 13:02:55 +0100
+
+soapdenovo2 (223-1) unstable; urgency=low
+
+ * Initial release (Closes: #700160)
+
+ -- Olivier Sallou <osallou at debian.org> Sat, 09 Feb 2013 10:40:45 +0100
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..45a4fb7
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+8
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..fa5d487
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,24 @@
+Source: soapdenovo2
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 8), hardening-includes, zlib1g-dev
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Olivier Sallou <osallou at debian.org>
+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}, zlib1g
+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.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..7b2a0a0
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,84 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: soapdenovo
+Source: http://soap.genomics.org.cn/soapdenovo.html
+
+Files: standardPregraph/inc/bam.h standardPregraph/inc/faidx.h sparsePregraph/inc/bam.h sparsePregraph/inc/faidx.h
+Copyright: 2008 Genome Research Ltd (GRL)
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
+
+Files: standardPregraph/inc/faidx.h sparsePregraph/inc/faidx.h
+Copyright: 2008 Broad Institute / Massachusetts Institute of Technology
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
+
+
+Files: *
+Copyright: 2008-2012 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 <osallou at debian.org>
+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".
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..bea77d9
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1 @@
+MANUAL
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..7d2fc41
--- /dev/null
+++ b/debian/install
@@ -0,0 +1,2 @@
+standardPregraph/SOAPdenovo-63mer usr/bin/
+standardPregraph/SOAPdenovo-127mer usr/bin/
diff --git a/debian/patches/add_hardening b/debian/patches/add_hardening
new file mode 100644
index 0000000..58f61a2
--- /dev/null
+++ b/debian/patches/add_hardening
@@ -0,0 +1,30 @@
+Subject: add fortify flags
+Description: Makefile does not load CFLAGS
+ from env, add extra flags for debian fortify
+Forwarded: no
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2013-02-09
+--- a/standardPregraph/Makefile
++++ b/standardPregraph/Makefile
+@@ -8,7 +8,11 @@
+ 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
++CFLAGS= -O4 -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2
++CFLAGS += `dpkg-buildflags --get CFLAGS` `dpkg-buildflags --get CPPFLAGS`
++CFLAGS+=$(HARDENING_CFLAGS)
++LDFLAGS = `dpkg-buildflags --get LDFLAGS`
++LDFLAGS+=$(HARDENING_LDFLAGS)
+ DFLAGS=
+ OBJS= arc.o attachPEinfo.o bubble.o check.o compactEdge.o \
+ concatenateEdge.o connect.o contig.o cutTipPreGraph.o cutTip_graph.o \
+@@ -81,7 +85,7 @@
+
+ SOAPdenovo: envTest $(OBJS)
+ @printf "Linking... \r"
+- @$(CC) $(CFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
++ @$(CC) $(CFLAGS) $(LDFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
+ @printf "$(PROG) compilation done.\n";
+
+ clean:
diff --git a/debian/patches/fix_gcc_path b/debian/patches/fix_gcc_path
new file mode 100644
index 0000000..556ddd9
--- /dev/null
+++ b/debian/patches/fix_gcc_path
@@ -0,0 +1,41 @@
+Subject: gcc wrong hard coded path
+Description: remove path for gcc
+Forwarded: yes
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2013-02-09
+--- 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 $(OBJS)
+ @printf "Linking... \r"
diff --git a/debian/patches/fix_usage_name b/debian/patches/fix_usage_name
new file mode 100644
index 0000000..fd20ec7
--- /dev/null
+++ b/debian/patches/fix_usage_name
@@ -0,0 +1,18 @@
+Subject: update binary name
+Description: usage show SOAPdenovo binary name
+ while generated binaries are kmer dependent.
+ Debian modification to lowercase applied too.
+Forwarded: no
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2013-02-09
+--- a/standardPregraph/main.c
++++ b/standardPregraph/main.c
+@@ -99,7 +99,7 @@
+
+ static void display_usage ()
+ {
+- fprintf ( stderr, "\nUsage: SOAPdenovo <command> [option]\n" );
++ fprintf ( stderr, "\nUsage: soapdenovo2-63mer/soapdenovo2-127mer <command> [option]\n" );
+ fprintf ( stderr, " pregraph construct kmer-graph\n" );
+ fprintf ( stderr, " contig eliminate errors and output contigs\n" );
+ fprintf ( stderr, " map map reads to contigs\n" );
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..f16b422
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,3 @@
+fix_gcc_path
+fix_usage_name
+add_hardening
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..0478a1a
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,34 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+export DEB_BUILD_HARDENING=1
+export DEB_BUILD_HARDENING_FORTIFY=1
+
+include /usr/share/hardening-includes/hardening.make
+
+CFLAGS=$(shell dpkg-buildflags --get CFLAGS)
+LDFLAGS=$(shell dpkg-buildflags --get LDFLAGS)
+CFLAGS+=$(HARDENING_CFLAGS)
+CXXFLAGS+=$(HARDENING_CXXFLAGS)
+LDFLAGS+=$(HARDENING_LDFLAGS)
+
+
+# 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
diff --git a/debian/soapdenovo2.1 b/debian/soapdenovo2.1
new file mode 100644
index 0000000..337618a
--- /dev/null
+++ b/debian/soapdenovo2.1
@@ -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
+
diff --git a/debian/soapdenovo2.manpages b/debian/soapdenovo2.manpages
new file mode 100644
index 0000000..8a8f173
--- /dev/null
+++ b/debian/soapdenovo2.manpages
@@ -0,0 +1 @@
+debian/soapdenovo2.1
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream b/debian/upstream
new file mode 100644
index 0000000..12c66d5
--- /dev/null
+++ b/debian/upstream
@@ -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
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..9854904
--- /dev/null
+++ b/debian/watch
@@ -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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