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debian/changelog
View file @ c0bbb786
abyss (2.2.3-2) unstable; urgency=medium
* Use libtext-multimarkdown-perl to obtain html documentation
Closes: #942908
* Standards-Version: 4.4.1
-- Andreas Tille <tille@debian.org> Sun, 15 Dec 2019 00:00:48 +0100
abyss (2.2.3-1) unstable; urgency=medium
* New upstream version
......
debian/control
View file @ c0bbb786
......@@ -5,7 +5,6 @@ Uploaders: Andreas Tille <tille@debian.org>,
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 12),
python-markdown,
libboost-graph-dev,
libopenmpi-dev,
libsparsehash-dev,
......@@ -13,7 +12,7 @@ Build-Depends: debhelper-compat (= 12),
libsqlite3-dev,
pkg-config,
help2man
Standards-Version: 4.4.0
Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/abyss
Vcs-Git: https://salsa.debian.org/med-team/abyss.git
Homepage: http://www.bcgsc.ca/platform/bioinfo/software/abyss
......
debian/patches/abyss-32-bit.patch deleted 100644 → 0
View file @ a5b116c8
Author: Graham Inggs <graham@nerve.org.za>
Last-Update: Thu, 16 Jul 2015 10:44:56 +0200
Forwarded: https://github.com/bcgsc/abyss/pull/278
Bug-Debian: http://bugs.debian.org/780409
Description: Fix FTBFS on 32-bit architectures
Version 1.5.2-1 of abyss FTBFS on 32-bit architectures (armhf, i386 and
powerpc). Previous versions built fine on all architectures.
.
There were a couple of places in the code that was introduced in version
1.5.2 where size_t data type was used instead of a fixed size data type.
The patch builds on amd64, i386 and armhf with and all unit tests passed.
.
Question: is this software useful on a 32-bit system at all?
--- a/Common/StringUtil.h
+++ b/Common/StringUtil.h
@@ -178,7 +178,7 @@ bool isReadNamePair(const std::string& n
return false;
}
-static inline size_t SIToBytes(std::istringstream& iss)
+static inline unsigned long long SIToBytes(std::istringstream& iss)
{
double size;
std::string units;
@@ -194,7 +194,7 @@ static inline size_t SIToBytes(std::istr
// no units given; clear fail flag
// and assume bytes
iss.clear(std::ios::eofbit);
- return (size_t)ceil(size);
+ return (unsigned long long)ceil(size);
}
if (units.size() > 1) {
debian/patches/gtest.patch deleted 100644 → 0
View file @ a5b116c8
Author: Anthony Raymond <traymond@bcgsc.ca>
Last-Updated: Wed, 17 Sep 2014 12:17:23 -0700
Description: Make sure gtest works properly
I had to follow the instructions on this post to build libgtest.a and libgtest_main.a:
http://askubuntu.com/questions/145887/why-no-library-files-installed-for-google-test
.
Attention: This patch needs heave adaption and is deactivated for the moment
--- a/Unittest/Makefile.am
+++ b/Unittest/Makefile.am
@@ -1,58 +1,72 @@
+check_LIBRARIES = libgtest.a libgtest_main.a
+
+gtest-all.cc:
+ cp $(GTEST)/src/gtest-all.cc .
+
+gtest_main.cc:
+ cp $(GTEST)/src/gtest_main.cc .
+
+libgtest_a_CPPFLAGS = -I$(top_srcdir) -I$(GTEST)
+libgtest_a_SOURCES = gtest-all.cc
+
+libgtest_main_a_CPPFLAGS = -I$(top_srcdir) -I$(GTEST)
+libgtest_main_a_SOURCES = gtest_main.cc gtest-all.cc
+
UNIT_TESTS = common_stringutil
check_PROGRAMS = common_stringutil
common_stringutil_SOURCES = Common/StringUtilTest.cpp
common_stringutil_CPPFLAGS = -I$(top_srcdir)
-common_stringutil_LDADD = $(GTEST_LIBS)
+common_stringutil_LDADD = libgtest_main.a $(GTEST_LIBS)
UNIT_TESTS += common_histogram
check_PROGRAMS += common_histogram
common_histogram_SOURCES = Common/HistogramTest.cpp
common_histogram_CPPFLAGS = -I$(top_srcdir)
-common_histogram_LDADD = $(GTEST_LIBS)
+common_histogram_LDADD = libgtest_main.a $(GTEST_LIBS)
UNIT_TESTS += common_bitutil
check_PROGRAMS += common_bitutil
common_bitutil_SOURCES = Common/BitUtilTest.cpp
common_bitutil_CPPFLAGS = -I$(top_srcdir)
-common_bitutil_LDADD = $(GTEST_LIBS)
+common_bitutil_LDADD = libgtest_main.a $(GTEST_LIBS)
UNIT_TESTS += common_kmer
check_PROGRAMS += common_kmer
common_kmer_SOURCES = Common/KmerTest.cpp
common_kmer_CPPFLAGS = -I$(top_srcdir)
-common_kmer_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
+common_kmer_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
UNIT_TESTS += common_sequence
check_PROGRAMS += common_sequence
common_sequence_SOURCES = Common/Sequence.cc
common_sequence_CPPFLAGS = -I$(top_srcdir)
-common_sequence_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
+common_sequence_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
UNIT_TESTS += common_KmerIterator
check_PROGRAMS += common_KmerIterator
common_KmerIterator_SOURCES = Common/KmerIteratorTest.cpp
common_KmerIterator_CPPFLAGS = -I$(top_srcdir)
-common_KmerIterator_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
+common_KmerIterator_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
UNIT_TESTS += common_sam
check_PROGRAMS += common_sam
common_sam_SOURCES = Common/SAM.cc
common_sam_CPPFLAGS = -I$(top_srcdir)
-common_sam_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
+common_sam_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
UNIT_TESTS += BloomFilter
check_PROGRAMS += BloomFilter
BloomFilter_SOURCES = Konnector/BloomFilter.cc
BloomFilter_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common
BloomFilter_CXXFLAGS = $(AM_CXXFLAGS) $(OPENMP_CXXFLAGS)
-BloomFilter_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
+BloomFilter_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
UNIT_TESTS += Konnector_DBGBloom
check_PROGRAMS += Konnector_DBGBloom
Konnector_DBGBloom_SOURCES = Konnector/DBGBloomTest.cpp
Konnector_DBGBloom_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common
Konnector_DBGBloom_CXXFLAGS = $(AM_CXXFLAGS) $(OPENMP_CXXFLAGS)
-Konnector_DBGBloom_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
+Konnector_DBGBloom_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
UNIT_TESTS += Konnector_DBGBloomAlgorithms
check_PROGRAMS += Konnector_DBGBloomAlgorithms
@@ -61,38 +75,38 @@ Konnector_DBGBloomAlgorithms_CPPFLAGS =
Konnector_DBGBloomAlgorithms_CXXFLAGS = $(AM_CXXFLAGS) $(OPENMP_CXXFLAGS)
Konnector_DBGBloomAlgorithms_LDADD = \
$(top_builddir)/Common/libcommon.a \
- $(GTEST_LIBS)
+ libgtest_main.a $(GTEST_LIBS)
UNIT_TESTS += graph_ConstrainedBFSVisitor
check_PROGRAMS += graph_ConstrainedBFSVisitor
graph_ConstrainedBFSVisitor_SOURCES = Graph/ConstrainedBFSVisitorTest.cpp
graph_ConstrainedBFSVisitor_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common
-graph_ConstrainedBFSVisitor_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
+graph_ConstrainedBFSVisitor_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
UNIT_TESTS += graph_BidirectionalBFS
check_PROGRAMS += graph_BidirectionalBFS
graph_BidirectionalBFS_SOURCES = Graph/BidirectionalBFSTest.cpp
graph_BidirectionalBFS_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common
-graph_BidirectionalBFS_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
+graph_BidirectionalBFS_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
UNIT_TESTS += graph_AllPathsSearch
check_PROGRAMS += graph_AllPathsSearch
graph_AllPathsSearch_SOURCES = Graph/AllPathsSearchTest.cpp
graph_AllPathsSearch_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common
-graph_AllPathsSearch_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
+graph_AllPathsSearch_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
UNIT_TESTS += graph_HashGraph
check_PROGRAMS += graph_HashGraph
graph_HashGraph_SOURCES = Graph/HashGraphTest.cpp
graph_HashGraph_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common
-graph_HashGraph_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
+graph_HashGraph_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
UNIT_TESTS += graph_ConstrainedBidiBFSVisitor
check_PROGRAMS += graph_ConstrainedBidiBFSVisitor
graph_ConstrainedBidiBFSVisitor_SOURCES = \
Graph/ConstrainedBidiBFSVisitorTest.cpp
graph_ConstrainedBidiBFSVisitor_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common
-graph_ConstrainedBidiBFSVisitor_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
+graph_ConstrainedBidiBFSVisitor_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
UNIT_TESTS += Konnector_konnector
check_PROGRAMS += Konnector_konnector
@@ -102,7 +116,7 @@ Konnector_konnector_CPPFLAGS = -I$(top_s
Konnector_konnector_CXXFLAGS = $(AM_CXXFLAGS) $(OPENMP_CXXFLAGS)
Konnector_konnector_LDADD = \
$(top_builddir)/Align/libalign.a \
- $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
+ $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
##Tests for log kmer counting / Counting bloom filter
--- a/configure.ac
+++ b/configure.ac
@@ -89,10 +89,12 @@ fi
# GTest
AC_ARG_WITH(gtest, AS_HELP_STRING([--with-gtest=PATH],
[specify prefix directory for the installed gtest library]))
+gtest_src="/usr/src/gtest"
if test "$with_gtest" -a -d "$with_gtest"; then
gtest_cppflags="-I$with_gtest/include"
- gtest_ldflags="-L$with_gtest/lib"
+ gtest_src="$with_gtest"
fi
+AC_SUBST(GTEST, "$gtest_src")
AC_ARG_ENABLE(mpich, AS_HELP_STRING([--enable-mpich],
[use MPICH (default is to use Open MPI)]))
@@ -118,7 +120,7 @@ boost_ver=1.55.0
boost_ver_dir=boost_1_55_0
AC_SUBST(CPPFLAGS,
"-I$my_abs_srcdir $boost_cppflags $mpi_cppflags $gtest_cppflags $CPPFLAGS -isystem$my_abs_srcdir/$boost_ver_dir")
-AC_SUBST(LDFLAGS, "$mpi_ldflags $gtest_ldflags $LDFLAGS")
+AC_SUBST(LDFLAGS, "$mpi_ldflags $LDFLAGS")
# Check for the MPI parallel computing library.
libs="$LIBS"
@@ -194,8 +196,7 @@ fi
libs="$LIBS"
AC_CHECK_HEADERS([gtest/gtest.h])
AC_CHECK_LIB([pthread], [pthread_create])
-AC_CHECK_LIB([gtest_main],[main])
-AM_CONDITIONAL([HAVE_GTEST], [test $ac_cv_header_gtest_gtest_h = yes -a $ac_cv_lib_gtest_main_main = yes])
+AM_CONDITIONAL([HAVE_GTEST], [test $ac_cv_header_gtest_gtest_h = yes])
AC_SUBST(GTEST_LIBS, "$LIBS")
LIBS=$libs
debian/rules
View file @ c0bbb786
......@@ -15,7 +15,7 @@ override_dh_auto_configure:
override_dh_auto_build:
dh_auto_build
markdown_py -f README.html README.md
markdown README.md > README.html
override_dh_auto_install:
dh_auto_install --destdir=debian/tmp
......
debian/upstream/metadata
View file @ c0bbb786
Name: ABySS
Reference:
Author: >
Jared T. Simpson and Kim Wong and Shaun D. Jackman and Jacqueline E. Schein
and Steven J.M. Jones and İnanç Birol
Title: "ABySS: A parallel assembler for short read sequence data"
Journal: Genome Research
Year: 2009
Volume: 19
Number: 6
Pages: 1117-23
PMID: 19251739
DOI: 10.1101/gr.089532.108
URL: http://genome.cshlp.org/content/19/6/1117
eprint: http://genome.cshlp.org/content/19/6/1117.full.pdf+html
Author: >
Jared T. Simpson and Kim Wong and Shaun D. Jackman and Jacqueline E. Schein
and Steven J.M. Jones and İnanç Birol
Title: "ABySS: A parallel assembler for short read sequence data"
Journal: Genome Research
Year: 2009
Volume: 19
Number: 6
Pages: 1117-23
PMID: 19251739
DOI: 10.1101/gr.089532.108
URL: http://genome.cshlp.org/content/19/6/1117
eprint: http://genome.cshlp.org/content/19/6/1117.full.pdf+html
Registry:
- Name: bio.tools
Entry: ABySS
- Name: OMICtools
Entry: OMICS_00006
- Name: SciCrunch
Entry: SCR_010709
- Name: conda:bioconda
Entry: abyss
Contact: Shaun Jackman <sjackman@gmail.com>
- Name: bio.tools
Entry: ABySS
- Name: OMICtools
Entry: OMICS_00006
- Name: SciCrunch
Entry: SCR_010709
- Name: conda:bioconda
Entry: abyss
Repository: https://github.com/bcgsc/abyss.git
Repository-Browse: https://github.com/bcgsc/abyss