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author | Marius Bakke <mbakke@fastmail.com> | 2018-10-22 23:07:16 +0200 |
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committer | Marius Bakke <mbakke@fastmail.com> | 2018-10-22 23:07:16 +0200 |
commit | c166a88dea354f0fb253e7d389e68f1b11fe1de4 (patch) | |
tree | 24719ff7ec1053c7e997afb10fe3a9bc276efddf /gnu/packages/patches | |
parent | ffddb42d6c510456997ee6de1c1b8026c9ce6d14 (diff) | |
parent | 63abd1e2a36d48e1f8f7057a4c844b9cf5733be7 (diff) | |
download | guix-patches-c166a88dea354f0fb253e7d389e68f1b11fe1de4.tar guix-patches-c166a88dea354f0fb253e7d389e68f1b11fe1de4.tar.gz |
Merge branch 'master' into core-updates
Diffstat (limited to 'gnu/packages/patches')
-rw-r--r-- | gnu/packages/patches/crossmap-allow-system-pysam.patch | 121 | ||||
-rw-r--r-- | gnu/packages/patches/delly-use-system-libraries.patch | 56 | ||||
-rw-r--r-- | gnu/packages/patches/liblxqt-include.patch | 14 | ||||
-rw-r--r-- | gnu/packages/patches/tophat-build-with-later-seqan.patch | 24 |
4 files changed, 0 insertions, 215 deletions
diff --git a/gnu/packages/patches/crossmap-allow-system-pysam.patch b/gnu/packages/patches/crossmap-allow-system-pysam.patch deleted file mode 100644 index 611c4ff74d..0000000000 --- a/gnu/packages/patches/crossmap-allow-system-pysam.patch +++ /dev/null @@ -1,121 +0,0 @@ -This patch modifies the build process such that the bundled copy of pysam does -not need to be built if CROSSMAP_USE_SYSTEM_PYSAM is set and the pysam module -can be imported. - -Upstream has agreed to apply the patch in the next maintenance release of -crossmap. The patch has already been uploaded to -http://sourceforge.net/projects/crossmap/files/patch/. - -diff --git a/setup.py b/setup.py ---- a/setup.py 2015-02-26 15:28:49.771189185 +0100 -+++ b/setup.py 2015-02-26 15:55:03.440327752 +0100 -@@ -19,6 +19,15 @@ - except: - have_numpy = False - -+try: -+ import pysam -+ if os.environ['CROSSMAP_USE_SYSTEM_PYSAM']: -+ have_pysam = True -+ else: -+ have_pysam = False -+except ImportError: -+ have_pysam = False -+ - if platform.system()=='Windows': - print >> sys.stderr, "Sorry, Windows platform is not supported!" - sys.exit() -@@ -165,49 +174,50 @@ - - - #================= pysam samtools ==================== -- extensions.append(Extension( -- "pysam.csamtools", -- csamtools_sources + [ "lib/pysam/%s" % x for x in ("pysam_util.c", )] +\ -- glob.glob( os.path.join( "lib/samtools", "*.pysam.c" )) +\ -- os_c_files + \ -- glob.glob( os.path.join( "lib/samtools", "*", "*.pysam.c" ) ), -- library_dirs=[], -- include_dirs=[ "lib/samtools", "lib/pysam" ] + include_os, -- libraries=[ "z", ], -- language="c", -- define_macros = [('_FILE_OFFSET_BITS','64'),('_USE_KNETFILE','')], -- )) -- -- extensions.append(Extension( -- "pysam.ctabix", -- tabix_sources + [ "lib/pysam/%s" % x for x in ( "tabix_util.c", )] +\ -- os_c_files + \ -- glob.glob( os.path.join( "lib/tabix", "*.pysam.c" ) ), -- library_dirs=[], -- include_dirs=[ "lib/tabix", "lib/pysam" ] + include_os, -- libraries=[ "z", ], -- language="c", -- define_macros = [('_FILE_OFFSET_BITS','64'), -- ('_USE_KNETFILE','')], -- )) -- -- extensions.append(Extension( -- "pysam.TabProxies", -- tabproxies_sources + os_c_files, -- library_dirs=[], -- include_dirs= include_os, -- libraries=[ "z", ], -- language="c", -- )) -- -- extensions.append(Extension( -- "pysam.cvcf", -- cvcf_sources + os_c_files, -- library_dirs=[], -- include_dirs= ["lib/tabix",] + include_os, -- libraries=[ "z", ], -- language="c", -- )) -+ if not have_pysam: -+ extensions.append(Extension( -+ "pysam.csamtools", -+ csamtools_sources + [ "lib/pysam/%s" % x for x in ("pysam_util.c", )] +\ -+ glob.glob( os.path.join( "lib/samtools", "*.pysam.c" )) +\ -+ os_c_files + \ -+ glob.glob( os.path.join( "lib/samtools", "*", "*.pysam.c" ) ), -+ library_dirs=[], -+ include_dirs=[ "lib/samtools", "lib/pysam" ] + include_os, -+ libraries=[ "z", ], -+ language="c", -+ define_macros = [('_FILE_OFFSET_BITS','64'),('_USE_KNETFILE','')], -+ )) -+ -+ extensions.append(Extension( -+ "pysam.ctabix", -+ tabix_sources + [ "lib/pysam/%s" % x for x in ( "tabix_util.c", )] +\ -+ os_c_files + \ -+ glob.glob( os.path.join( "lib/tabix", "*.pysam.c" ) ), -+ library_dirs=[], -+ include_dirs=[ "lib/tabix", "lib/pysam" ] + include_os, -+ libraries=[ "z", ], -+ language="c", -+ define_macros = [('_FILE_OFFSET_BITS','64'), -+ ('_USE_KNETFILE','')], -+ )) -+ -+ extensions.append(Extension( -+ "pysam.TabProxies", -+ tabproxies_sources + os_c_files, -+ library_dirs=[], -+ include_dirs= include_os, -+ libraries=[ "z", ], -+ language="c", -+ )) -+ -+ extensions.append(Extension( -+ "pysam.cvcf", -+ cvcf_sources + os_c_files, -+ library_dirs=[], -+ include_dirs= ["lib/tabix",] + include_os, -+ libraries=[ "z", ], -+ language="c", -+ )) - - - return extensions diff --git a/gnu/packages/patches/delly-use-system-libraries.patch b/gnu/packages/patches/delly-use-system-libraries.patch deleted file mode 100644 index 3315c2a176..0000000000 --- a/gnu/packages/patches/delly-use-system-libraries.patch +++ /dev/null @@ -1,56 +0,0 @@ ---- a/Makefile 2017-04-09 12:48:15.000000000 +0200 -+++ b/Makefile 2017-06-21 14:26:02.749282787 +0200 -@@ -9,8 +9,8 @@ - - # Flags - CXX=g++ --CXXFLAGS += -isystem ${SEQTK_ROOT} -isystem ${BOOST_ROOT} -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing --LDFLAGS += -L${SEQTK_ROOT} -L${BOOST_ROOT}/stage/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time -+CXXFLAGS += -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing -+LDFLAGS += -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time - - # Additional flags for release/debug - ifeq (${PARALLEL}, 1) -@@ -23,7 +23,7 @@ - ifeq (${STATIC}, 1) - LDFLAGS += -static -static-libgcc -pthread -lhts -lz - else -- LDFLAGS += -lhts -lz -Wl,-rpath,${SEQTK_ROOT},-rpath,${BOOST_ROOT}/stage/lib -+ LDFLAGS += -lhts -lz - endif - ifeq (${DEBUG}, 1) - CXXFLAGS += -g -O0 -fno-inline -DDEBUG -@@ -41,29 +41,17 @@ - DELLYSOURCES = $(wildcard src/*.h) $(wildcard src/*.cpp) - - # Targets --TARGETS = .htslib .bcftools .boost src/delly src/cov src/dpe -+TARGETS = src/delly src/cov src/dpe - - all: $(TARGETS) - --.htslib: $(HTSLIBSOURCES) -- cd src/htslib && make && make lib-static && cd ../../ && touch .htslib -- --.bcftools: $(HTSLIBSOURCES) -- cd src/bcftools && make && cd ../../ && touch .bcftools -- --.boost: $(BOOSTSOURCES) -- cd src/modular-boost && ./bootstrap.sh --prefix=${PWD}/src/modular-boost --without-icu --with-libraries=iostreams,filesystem,system,program_options,date_time && ./b2 && ./b2 headers && cd ../../ && touch .boost -- --src/delly: .htslib .bcftools .boost $(DELLYSOURCES) -- $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) -- --src/cov: .htslib .bcftools .boost $(DELLYSOURCES) -+src/cov: $(DELLYSOURCES) - $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) - --src/dpe: .htslib .bcftools .boost $(DELLYSOURCES) -+src/dpe: $(DELLYSOURCES) - $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) - - clean: - cd src/htslib && make clean - cd src/modular-boost && ./b2 --clean-all -- rm -f $(TARGETS) $(TARGETS:=.o) .htslib .boost .bcftools -+ rm -f $(TARGETS) $(TARGETS:=.o) diff --git a/gnu/packages/patches/liblxqt-include.patch b/gnu/packages/patches/liblxqt-include.patch deleted file mode 100644 index 4e8cf04789..0000000000 --- a/gnu/packages/patches/liblxqt-include.patch +++ /dev/null @@ -1,14 +0,0 @@ -Patch to fix build with Qt 5.5, taken from upstream: - https://github.com/lxde/liblxqt/commit/7303ea207de0771d6f450a31ec4a1ce69202869b - -diff -u -r liblxqt-0.9.0.orig/lxqtnotification.h liblxqt-0.9.0/lxqtnotification.h ---- liblxqt-0.9.0.orig/lxqtnotification.h 2015-07-27 22:49:05.365166482 +0200 -+++ liblxqt-0.9.0/lxqtnotification.h 2015-07-27 22:49:36.897606619 +0200 -@@ -25,6 +25,7 @@ - #ifndef LXQTNOTIFICATION_H - #define LXQTNOTIFICATION_H - -+#include <QObject> - #include <QStringList> - #include "lxqtglobals.h" - diff --git a/gnu/packages/patches/tophat-build-with-later-seqan.patch b/gnu/packages/patches/tophat-build-with-later-seqan.patch deleted file mode 100644 index fc742e2a7d..0000000000 --- a/gnu/packages/patches/tophat-build-with-later-seqan.patch +++ /dev/null @@ -1,24 +0,0 @@ -This patch resolves a build failure when building TopHat 2.1.0 with SeqAn 1.4. -This is the relevant part of a patch originally posted here: -https://lists.fu-berlin.de/pipermail/seqan-dev/2014-July/msg00001.html - ---- a/src/segment_juncs.cpp -+++ b/src/segment_juncs.cpp -@@ -2050,10 +2050,13 @@ void juncs_from_ref_segs(RefSequenceTabl - typedef map<uint32_t, IntronMotifs> MotifMap; - - MotifMap ims; -- -- seqan::DnaStringReverseComplement rev_donor_dinuc(donor_dinuc); -- seqan::DnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc); -- -+ -+ typedef seqan::ModifiedString< -+ seqan::ModifiedString<seqan::DnaString const, seqan::ModView<seqan::FunctorComplement<seqan::Dna> > >, -+ seqan::ModReverse> ConstDnaStringReverseComplement; -+ ConstDnaStringReverseComplement rev_donor_dinuc(donor_dinuc); -+ ConstDnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc); -+ - if (talkative) - fprintf(stderr, "Collecting potential splice sites in islands\n"); - |