debian/ 0000755 0000000 0000000 00000000000 12177737344 007205 5 ustar debian/source/ 0000755 0000000 0000000 00000000000 12177737344 010505 5 ustar debian/source/format 0000644 0000000 0000000 00000000014 12105425570 011675 0 ustar 3.0 (quilt)
debian/copyright 0000644 0000000 0000000 00000011024 12177735440 011131 0 ustar 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/compat 0000644 0000000 0000000 00000000002 12177702230 010365 0 ustar 9
debian/watch 0000644 0000000 0000000 00000000313 12131276267 010223 0 ustar # 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/docs 0000644 0000000 0000000 00000000007 12105425570 010037 0 ustar MANUAL
debian/soapdenovo2.manpages 0000644 0000000 0000000 00000000025 12105425570 013140 0 ustar debian/soapdenovo2.1
debian/patches/ 0000755 0000000 0000000 00000000000 12177737344 010634 5 ustar debian/patches/use_debian_zlib 0000644 0000000 0000000 00000015726 12177732016 013677 0 ustar 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/series 0000644 0000000 0000000 00000000110 12177735521 012034 0 ustar use_libsam
fix_compilation
fix_usage_name
add_hardening
use_debian_zlib
debian/patches/fix_compilation 0000644 0000000 0000000 00000002315 12177715367 013745 0 ustar 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_name 0000644 0000000 0000000 00000001356 12163046034 013516 0 ustar 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_libsam 0000644 0000000 0000000 00000002232 12177736536 012703 0 ustar 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_hardening 0000644 0000000 0000000 00000006700 12177715373 013327 0 ustar 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.Debian 0000644 0000000 0000000 00000000423 12105426313 011223 0 ustar * 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/install 0000644 0000000 0000000 00000000065 12177702071 010564 0 ustar SOAPdenovo-63mer usr/bin/
SOAPdenovo-127mer usr/bin/
debian/soapdenovo2.1 0000644 0000000 0000000 00000002460 12105425570 011512 0 ustar .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/control 0000644 0000000 0000000 00000002067 12177712777 010620 0 ustar 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}, ${misc:Depends}, zlib1g
Description: short-read assembly method to build de novo draft assembly
SOAPdenovo is a novel short-read assembly method that can build a de novo draft
assembly for the human-sized genomes. The program is specially designed to
assemble Illumina GA short reads.
.
It creates new opportunities for building reference
sequences and carrying out accurate analyses of unexplored genomes in a cost
effective way.
debian/rules 0000755 0000000 0000000 00000001441 12177711247 010257 0 ustar #!/usr/bin/make -f
# -*- makefile -*-
export DEB_BUILD_HARDENING=1
export DEB_BUILD_HARDENING_FORTIFY=1
include /usr/share/hardening-includes/hardening.make
CFLAGS=$(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/upstream 0000644 0000000 0000000 00000001323 12130776571 010761 0 ustar 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/changelog 0000644 0000000 0000000 00000001453 12177737323 011057 0 ustar 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