debian/0000755000000000000000000000000012177737344007205 5ustar debian/source/0000755000000000000000000000000012177737344010505 5ustar debian/source/format0000644000000000000000000000001412105425570011675 0ustar 3.0 (quilt) debian/copyright0000644000000000000000000001102412177735440011131 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: soapdenovo Source: http://soap.genomics.org.cn/soapdenovo.html Files-Excluded: standardPregraph/*.a standardPregraph/inc/sam.h standardPregraph/inc/bam.h standardPregraph/inc/bgzf.h sparsePregraph/inc/sam.h sparsePregraph/inc/bam.h sparsePregraph/inc/bgzf.h standardPregraph/inc/zlib.h standardPregraph/inc/zconf.h sparsePregraph/inc/zlib.h sparsePregraph/inc/zconf.h standardPregraph/inc/*.so sparsePregraph/*.a 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 . 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 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 . On Debian systems, the complete text of the GNU General Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". debian/compat0000644000000000000000000000000212177702230010365 0ustar 9 debian/watch0000644000000000000000000000031312131276267010223 0ustar # Compulsory line, this is a version 3 file version=3 opts="dversionmangle=s/\+dfsg//g" http://qa.debian.org/watch/sf.php/soapdenovo2/SOAPdenovo2-src-r(.+)\.(?:zip|tgz|tbz2|txz|tar\.gz|tar\.bz2|tar\.xz) debian/docs0000644000000000000000000000000712105425570010037 0ustar MANUAL debian/soapdenovo2.manpages0000644000000000000000000000002512105425570013140 0ustar debian/soapdenovo2.1 debian/patches/0000755000000000000000000000000012177737344010634 5ustar debian/patches/use_debian_zlib0000644000000000000000000001572612177732016013677 0ustar Subject: use Debian zlib library Description: Debian library is more recent than the one embedded upstream. Its API changed and code needs to be updated to use this version. See more info here: http://www.postgresql.org/message-id/1329988571.6474.9.camel@vanquo.pezone.net Author: Olivier Sallou Last-Updated: 2013-08-05 Forwaded: no --- a/standardPregraph/prlRead2Ctg.c +++ b/standardPregraph/prlRead2Ctg.c @@ -424,7 +424,7 @@ } } -static void output1read_gz ( int t, gzFile * outfp, gzFile * outfp2, char orien, int dhflag ) +static void output1read_gz ( int t, gzFile outfp, gzFile outfp2, char orien, int dhflag ) { int len = lenBuffer[t]; int index; @@ -500,7 +500,7 @@ fprintf ( outfp, "\n" ); } -static void getPEreadOnContig ( int t, gzFile * outfp ) +static void getPEreadOnContig ( int t, gzFile outfp ) { int len1, len2, index; char orien1, orien2; @@ -560,7 +560,7 @@ } }*/ -static void getReadIngap ( int t, int insSize, gzFile * outfp1, gzFile * outfp2, boolean readOne ) +static void getReadIngap ( int t, int insSize, gzFile outfp1, gzFile outfp2, boolean readOne ) { int read1, read2; char orientation; @@ -618,7 +618,7 @@ } } -static void recordAlldgn ( gzFile * outfp, int * insSizeArr, gzFile * outfp1, gzFile * outfp2, gzFile * outfp4 ) +static void recordAlldgn ( gzFile outfp, int * insSizeArr, gzFile outfp1, gzFile outfp2, gzFile outfp4 ) { int t, ctgId; boolean rd1gap, rd2gap; @@ -773,7 +773,7 @@ long long i; char * src_name, *next_name, name[256]; FILE * fo2; - gzFile * fo, *outfp1 = NULL, *outfp2 = NULL, *outfp3 = NULL, *outfp4 = NULL; + gzFile fo, outfp1 = NULL, outfp2 = NULL, outfp3 = NULL, outfp4 = NULL; int maxReadNum, libNo, prevLibNo, insSize = 0; boolean flag, pairs = 1; pthread_t threads[thrd_num]; --- a/standardPregraph/prlReadFillGap.c +++ b/standardPregraph/prlReadFillGap.c @@ -104,7 +104,7 @@ free ( ( void * ) length_array ); } -static long long getRead1by1_gz ( gzFile * fp, DARRAY * readSeqInGap ) +static long long getRead1by1_gz ( gzFile fp, DARRAY * readSeqInGap ) { long long readCounter = 0; @@ -206,7 +206,7 @@ static boolean loadReads4gap ( char * graphfile ) { FILE * fp1, *fp2; - gzFile * fp; + gzFile fp; char name[1024]; long long readCounter; --- a/standardPregraph/output_pregraph.c +++ b/standardPregraph/output_pregraph.c @@ -85,7 +85,7 @@ fclose ( fp ); } -void output_1edge ( preEDGE * edge, gzFile * fp ) +void output_1edge ( preEDGE * edge, gzFile fp ) { int i; gzprintf ( fp, ">length %d,", edge->length ); --- a/standardPregraph/orderContig.c +++ b/standardPregraph/orderContig.c @@ -5072,7 +5072,7 @@ char name[256], *line; FILE * fp1; FILE * linkF; - gzFile * fp2; + gzFile fp2; int i; int flag = 0; unsigned int j; --- a/standardPregraph/node2edge.c +++ b/standardPregraph/node2edge.c @@ -37,8 +37,8 @@ static preEDGE temp_edge; // for temp use in merge_V2() static char edge_seq[100000]; //use this static 'edge_seq ' as an temp seq in merge_V2() for speed .. -static void make_edge ( gzFile * fp ); -static void merge_linearV2 ( char bal_edge, STACK * nStack, int count, gzFile * fp ); +static void make_edge ( gzFile fp ); +static void merge_linearV2 ( char bal_edge, STACK * nStack, int count, gzFile fp ); static int check_iden_kmerList ( STACK * stack1, STACK * stack2 ); //for stack @@ -60,7 +60,7 @@ *************************************************/ void kmer2edges ( char * outfile ) { - gzFile * fp; + gzFile fp; char temp[256]; sprintf ( temp, "%s.edge.gz", outfile ); fp = gzopen ( temp, "w" ); @@ -234,7 +234,7 @@ Return: 0. *************************************************/ -static int startEdgeFromNode ( kmer_t * node1, gzFile * fp ) +static int startEdgeFromNode ( kmer_t * node1, gzFile fp ) { int node_c, palindrome; unsigned char flag; @@ -363,7 +363,7 @@ Return: None. *************************************************/ -void make_edge ( gzFile * fp ) +void make_edge ( gzFile fp ) { int i = 0; kmer_t * node1; @@ -427,7 +427,7 @@ Return: None. *************************************************/ -static void merge_linearV2 ( char bal_edge, STACK * nStack, int count, gzFile * fp ) +static void merge_linearV2 ( char bal_edge, STACK * nStack, int count, gzFile fp ) { int length, char_index; preEDGE * newedge; --- a/standardPregraph/loadPreGraph.c +++ b/standardPregraph/loadPreGraph.c @@ -449,7 +449,7 @@ { char c, name[256], line[1024], str[32]; char * tightSeq = NULL; - gzFile * fp; + gzFile fp; Kmer from_kmer, to_kmer; int n = 0, i, length, cvg, index = -1, bal_ed, edgeno; int linelen; --- a/standardPregraph/kmer.c +++ b/standardPregraph/kmer.c @@ -483,7 +483,7 @@ fprintf ( fp, "%c", c ); } -void print_kmer_gz ( gzFile * fp, Kmer kmer, char c ) +void print_kmer_gz ( gzFile fp, Kmer kmer, char c ) { gzprintf ( fp, "%llx %llx %llx %llx", kmer.high1, kmer.low1, kmer.high2, kmer.low2 ); gzprintf ( fp, "%c", c ); @@ -795,7 +795,7 @@ fprintf ( fp, "%c", c ); } -void print_kmer_gz ( gzFile * fp, Kmer kmer, char c ) +void print_kmer_gz ( gzFile fp, Kmer kmer, char c ) { gzprintf ( fp, "%llx %llx", kmer.high, kmer.low ); gzprintf ( fp, "%c", c ); --- a/standardPregraph/attachPEinfo.c +++ b/standardPregraph/attachPEinfo.c @@ -492,7 +492,7 @@ Return: Loaded alignment record number. *************************************************/ -int connectByPE_grad_gz ( gzFile * fp, int peGrad, char * line ) +int connectByPE_grad_gz ( gzFile fp, int peGrad, char * line ) { long long pre_readno, readno, minno, maxno; int pre_pos, pos, flag, PE, count = 0, Total_PE = 0; --- a/standardPregraph/inc/extfunc.h +++ b/standardPregraph/inc/extfunc.h @@ -79,10 +79,10 @@ extern int putInsertS ( long long readid, int size, int * currGrads ); extern int getInsertS ( long long readid, int * readlen ); extern int connectByPE_grad ( FILE * fp, int peGrad, char * line ); -extern int connectByPE_grad_gz ( gzFile * fp, int peGrad, char * line ); +extern int connectByPE_grad_gz ( gzFile fp, int peGrad, char * line ); extern void PEgradsScaf ( char * infile ); extern void reorderAnnotation ( char * infile, char * outfile ); -extern void output_1edge ( preEDGE * edge, gzFile * fp ); +extern void output_1edge ( preEDGE * edge, gzFile fp ); extern void prlRead2edge ( char * libfile, char * outfile ); extern void annotFileTrans ( char * infile, char * outfile ); extern void prlLoadPath ( char * graphfile ); --- a/standardPregraph/hashFunction.c +++ b/standardPregraph/hashFunction.c @@ -82,7 +82,7 @@ }; typedef int ( *CRC32CFunctionPtr ) ( uint32_t, const char *, size_t ); -static CRC32CFunctionPtr crc32; +static CRC32CFunctionPtr s_crc32; static uint32_t cpuid ( uint32_t functionInput ) { @@ -145,11 +145,11 @@ ubyte8 hash_kmer ( Kmer kmer ) { - return ( crc32 ( 0, ( char * ) &kmer, sizeof ( Kmer ) ) ); + return ( s_crc32 ( 0, ( char * ) &kmer, sizeof ( Kmer ) ) ); } void crc32c_Init() { - crc32 = detectBestCRC32C(); + s_crc32 = detectBestCRC32C(); } debian/patches/series0000644000000000000000000000011012177735521012034 0ustar use_libsam fix_compilation fix_usage_name add_hardening use_debian_zlib debian/patches/fix_compilation0000644000000000000000000000231512177715367013745 0ustar Subject: Fails to compile, usleep unknown Description: code from upstream fails to compile. An include is missing. Mail has been sent upstream and question posted to their google group but got no answer. Forwarded: no Author: Olivier Sallou Last-Updated: 2013-08-05 --- a/sparsePregraph/pregraph_sparse.cpp +++ b/sparsePregraph/pregraph_sparse.cpp @@ -32,6 +32,7 @@ #include "seq_util.h" #include "convert_soapdenovo.h" +#include static int LOAD_GRAPH = 0, BUILD_DBG = 1, BUILD_EDGES = 1, BUILD_PREARCS = 1; //static int run_mode=0; --- a/sparsePregraph/inc/multi_threads.h +++ b/sparsePregraph/inc/multi_threads.h @@ -24,6 +24,8 @@ #define _MULTI_THREADS_H #include "stdinc.h" +#include + typedef struct parameter { unsigned char threadID; --- a/Makefile +++ b/Makefile @@ -7,7 +7,7 @@ SUBDIRS = sparsePregraph standardPregraph PROG= SOAPdenovo-63mer SOAPdenovo-127mer -INCLUDES= -I./sparsePregraph/inc -I./standardPregraph/inc +INCLUDES= -I./sparsePregraph/inc -I./standardPregraph/inc -I/usr/include/x86_64-linux-gnu LIBPATH= -L/lib64 -L/usr/lib64 -L./sparsePregraph/inc -L./standardPregraph/inc LIBS= -pthread -lz -lm debian/patches/fix_usage_name0000644000000000000000000000135612163046034013516 0ustar 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 Last-Updated: 2013-02-09 --- a/standardPregraph/main.c +++ b/standardPregraph/main.c @@ -104,7 +104,7 @@ static void display_usage () { - fprintf ( stderr, "\nUsage: SOAPdenovo [option]\n" ); + fprintf ( stderr, "\nUsage: soapdenovo2-63mer/soapdenovo2-127mer [option]\n" ); fprintf ( stderr, " pregraph construct kmer-graph\n" ); fprintf ( stderr, " sparse_pregraph construct sparse kmer-graph\n"); fprintf ( stderr, " contig eliminate errors and output contigs\n" ); debian/patches/use_libsam0000644000000000000000000000223212177736536012703 0ustar Subject: upstream copies libsam headers Description: use Debian libraries instead of embedded headers Author: Olivier Sallou Last-Updated: 2013-08-05 Forwarded: no --- a/sparsePregraph/Makefile +++ b/sparsePregraph/Makefile @@ -10,7 +10,7 @@ build_preArc.o pregraph_sparse.o io_func.o\ global.o convert_soapdenovo.o PROG= -INCLUDES= -I./inc +INCLUDES= -I./inc -I/usr/include/samtools SUBDIRS= . LIBPATH= -L/usr/lib64 LIBS= -pthread -lz -L./inc --- a/sparsePregraph/inc/stdinc.h +++ b/sparsePregraph/inc/stdinc.h @@ -39,4 +39,4 @@ - +#include --- a/standardPregraph/Makefile +++ b/standardPregraph/Makefile @@ -25,7 +25,7 @@ readseq1by1.o scaffold.o searchPath.o seq.o splitReps.o \ cutTip_graph2.o linearEdge.o kmerhash.o read2edge.o iterate.o PROG= SOAPdenovo-63mer -INCLUDES= -Iinc +INCLUDES= -Iinc -I/usr/include/samtools SUBDIRS= . LIBPATH= -L/lib64 -L/usr/lib64 -L./inc LIBS= -pthread -lz -lm --- a/standardPregraph/inc/stdinc.h +++ b/standardPregraph/inc/stdinc.h @@ -32,3 +32,4 @@ #include "types.h" #include #include +#include debian/patches/add_hardening0000644000000000000000000000670012177715373013327 0ustar Subject: add fortify flags Description: Makefile does not load CFLAGS from env, add extra flags for debian fortify Forwarded: no Author: Olivier Sallou Last-Updated: 2013-02-09 --- a/standardPregraph/Makefile +++ b/standardPregraph/Makefile @@ -12,7 +12,11 @@ CFLAGS= -O0 -g -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2 else CFLAGS= -O4 -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2 +CFLAGS+= `dpkg-buildflags --get CFLAGS` `dpkg-buildflags --get CPPFLAGS` +CFLAGS+=$(HARDENING_CFLAGS) endif +LDFLAGS= `dpkg-buildflags --get LDFLAGS` +LDFLAGS+=$(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 \ @@ -87,9 +91,10 @@ @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) +#SOAPdenovo: envTest $(OBJS) +SOAPdenovo: @printf "Linking... \r" - @$(CC) $(CFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS) + @$(CC) $(CFLAGS) $(LDFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS) @printf "$(PROG) compilation done.\n"; clean: --- a/sparsePregraph/Makefile +++ b/sparsePregraph/Makefile @@ -3,7 +3,11 @@ CFLAGS= -O0 -g -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2 else CFLAGS= -O4 -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2 +CFLAGS+= `dpkg-buildflags --get CFLAGS` `dpkg-buildflags --get CPPFLAGS` +CFLAGS+=$(HARDENING_CFLAGS) endif +LDFLAGS= `dpkg-buildflags --get LDFLAGS` +LDFLAGS+=$(HARDENING_LDFLAGS) DFLAGS= OBJS= build_graph.o build_edge.o multi_threads.o \ @@ -74,7 +78,7 @@ pregraph_sparse: clean envTest $(OBJS) @printf "Linking... \r" - #@$(CC) $(CFLAGS)$(INCLUDES) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS) + #@$(CC) $(LDFLAGS) $(CFLAGS)$(INCLUDES) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS) @printf "$(PROG) compilation done.\n"; clean: --- a/Makefile +++ b/Makefile @@ -3,8 +3,13 @@ CFLAGS= -O0 -g -fomit-frame-pointer else CFLAGS= -O4 -fomit-frame-pointer +CFLAGS+= `dpkg-buildflags --get CFLAGS` `dpkg-buildflags --get CPPFLAGS` +CFLAGS+=$(HARDENING_CFLAGS) endif +LDFLAGS= `dpkg-buildflags --get LDFLAGS` +LDFLAGS+=$(HARDENING_LDFLAGS) + SUBDIRS = sparsePregraph standardPregraph PROG= SOAPdenovo-63mer SOAPdenovo-127mer INCLUDES= -I./sparsePregraph/inc -I./standardPregraph/inc -I/usr/include/x86_64-linux-gnu @@ -64,11 +69,11 @@ SOAPdenovo-63mer: @cd sparsePregraph;make 63mer=1;cd ..; @cd standardPregraph;make 63mer=1;cd ..; - @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer + @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LDFLAGS) $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer SOAPdenovo-127mer: @cd sparsePregraph;make 127mer=1;cd ..; @cd standardPregraph;make 127mer=1;cd ..; - @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer + @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LDFLAGS) $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer clean: @cd sparsePregraph;make clean;cd ..; @cd standardPregraph;make clean;cd ..; debian/README.Debian0000644000000000000000000000042312105426313011223 0ustar * 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 Sat, 09 Feb 2013 10:40:45 +0100 debian/install0000644000000000000000000000006512177702071010564 0ustar SOAPdenovo-63mer usr/bin/ SOAPdenovo-127mer usr/bin/ debian/soapdenovo2.10000644000000000000000000000246012105425570011512 0ustar .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 debian/control0000644000000000000000000000206712177712777010620 0ustar Source: soapdenovo2 Section: science Priority: optional Build-Depends: debhelper (>= 9), hardening-includes, zlib1g-dev, libbam-dev, libaio-dev Maintainer: Debian Med Packaging Team Uploaders: Olivier Sallou Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/soap/soapdenovo2/trunk/ Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/soap/soapdenovo2/ Standards-Version: 3.9.4 Homepage: http://soap.genomics.org.cn/soapdenovo.html Package: soapdenovo2 Architecture: any-amd64 any-ppc64 any-ia64 #Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, zlib1g Description: short-read assembly method to build de novo draft assembly SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. . It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. debian/rules0000755000000000000000000000144112177711247010257 0ustar #!/usr/bin/make -f # -*- makefile -*- export DEB_BUILD_HARDENING=1 export DEB_BUILD_HARDENING_FORTIFY=1 include /usr/share/hardening-includes/hardening.make CFLAGS=$(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 debian/upstream0000644000000000000000000000132312130776571010761 0ustar 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 debian/changelog0000644000000000000000000000145312177737323011057 0ustar soapdenovo2 (240+dfsg-1) unstable; urgency=low * New upstream release -- Olivier Sallou Thu, 27 Jun 2013 16:23:26 +0200 soapdenovo2 (223+dfsg-1) unstable; urgency=low * debian/copyright: remove .a files from upstream archive (Closes: #705139). debian/patches: update patches after lib removal debian/control: add bam and aio lib dependencies -- Olivier Sallou Wed, 10 Apr 2013 17:27:22 +0200 soapdenovo2 (223-2) unstable; urgency=low * debian/copyright: Update copyright years and content, -- Olivier Sallou Sat, 09 Feb 2013 13:02:55 +0100 soapdenovo2 (223-1) unstable; urgency=low * Initial release (Closes: #700160) -- Olivier Sallou Sat, 09 Feb 2013 10:40:45 +0100