diff options
Diffstat (limited to 'gnu/packages/patches')
| -rw-r--r-- | gnu/packages/patches/crossmap-allow-system-pysam.patch | 121 |
1 files changed, 0 insertions, 121 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 |