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-rw-r--r--gnu/packages/patches/crossmap-allow-system-pysam.patch121
-rw-r--r--gnu/packages/patches/delly-use-system-libraries.patch56
-rw-r--r--gnu/packages/patches/liblxqt-include.patch14
-rw-r--r--gnu/packages/patches/tophat-build-with-later-seqan.patch24
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");
-
generated by cgit v1.2.3 (git 2.45.0) at 2024-12-18 05:16:22 +0000