191c710139
* gnu/packages/bioinformatics.scm (crossmap): New variable. * gnu/packages/patches/crossmap-allow-system-pysam.patch: New file. * gnu-system.am (dist_patch_DATA): Add it.
121 lines
4.4 KiB
Diff
121 lines
4.4 KiB
Diff
This patch modifies the build process such that the bundled copy of pysam does
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not need to be built if CROSSMAP_USE_SYSTEM_PYSAM is set and the pysam module
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can be imported.
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Upstream has agreed to apply the patch in the next maintenance release of
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crossmap. The patch has already been uploaded to
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http://sourceforge.net/projects/crossmap/files/patch/.
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diff --git a/setup.py b/setup.py
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--- a/setup.py 2015-02-26 15:28:49.771189185 +0100
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+++ b/setup.py 2015-02-26 15:55:03.440327752 +0100
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@@ -19,6 +19,15 @@
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except:
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have_numpy = False
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+try:
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+ import pysam
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+ if os.environ['CROSSMAP_USE_SYSTEM_PYSAM']:
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+ have_pysam = True
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+ else:
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+ have_pysam = False
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+except ImportError:
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+ have_pysam = False
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+
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if platform.system()=='Windows':
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print >> sys.stderr, "Sorry, Windows platform is not supported!"
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sys.exit()
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@@ -165,49 +174,50 @@
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#================= pysam samtools ====================
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- extensions.append(Extension(
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- "pysam.csamtools",
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- csamtools_sources + [ "lib/pysam/%s" % x for x in ("pysam_util.c", )] +\
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- glob.glob( os.path.join( "lib/samtools", "*.pysam.c" )) +\
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- os_c_files + \
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- glob.glob( os.path.join( "lib/samtools", "*", "*.pysam.c" ) ),
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- library_dirs=[],
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- include_dirs=[ "lib/samtools", "lib/pysam" ] + include_os,
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- libraries=[ "z", ],
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- language="c",
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- define_macros = [('_FILE_OFFSET_BITS','64'),('_USE_KNETFILE','')],
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- ))
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-
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- extensions.append(Extension(
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- "pysam.ctabix",
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- tabix_sources + [ "lib/pysam/%s" % x for x in ( "tabix_util.c", )] +\
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- os_c_files + \
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- glob.glob( os.path.join( "lib/tabix", "*.pysam.c" ) ),
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- library_dirs=[],
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- include_dirs=[ "lib/tabix", "lib/pysam" ] + include_os,
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- libraries=[ "z", ],
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- language="c",
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- define_macros = [('_FILE_OFFSET_BITS','64'),
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- ('_USE_KNETFILE','')],
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- ))
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-
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- extensions.append(Extension(
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- "pysam.TabProxies",
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- tabproxies_sources + os_c_files,
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- library_dirs=[],
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- include_dirs= include_os,
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- libraries=[ "z", ],
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- language="c",
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- ))
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-
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- extensions.append(Extension(
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- "pysam.cvcf",
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- cvcf_sources + os_c_files,
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- library_dirs=[],
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- include_dirs= ["lib/tabix",] + include_os,
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- libraries=[ "z", ],
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- language="c",
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- ))
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+ if not have_pysam:
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+ extensions.append(Extension(
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+ "pysam.csamtools",
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+ csamtools_sources + [ "lib/pysam/%s" % x for x in ("pysam_util.c", )] +\
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+ glob.glob( os.path.join( "lib/samtools", "*.pysam.c" )) +\
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+ os_c_files + \
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+ glob.glob( os.path.join( "lib/samtools", "*", "*.pysam.c" ) ),
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+ library_dirs=[],
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+ include_dirs=[ "lib/samtools", "lib/pysam" ] + include_os,
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+ libraries=[ "z", ],
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+ language="c",
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+ define_macros = [('_FILE_OFFSET_BITS','64'),('_USE_KNETFILE','')],
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+ ))
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+
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+ extensions.append(Extension(
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+ "pysam.ctabix",
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+ tabix_sources + [ "lib/pysam/%s" % x for x in ( "tabix_util.c", )] +\
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+ os_c_files + \
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+ glob.glob( os.path.join( "lib/tabix", "*.pysam.c" ) ),
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+ library_dirs=[],
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+ include_dirs=[ "lib/tabix", "lib/pysam" ] + include_os,
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+ libraries=[ "z", ],
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+ language="c",
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+ define_macros = [('_FILE_OFFSET_BITS','64'),
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+ ('_USE_KNETFILE','')],
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+ ))
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+
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+ extensions.append(Extension(
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+ "pysam.TabProxies",
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+ tabproxies_sources + os_c_files,
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+ library_dirs=[],
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+ include_dirs= include_os,
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+ libraries=[ "z", ],
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+ language="c",
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+ ))
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+
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+ extensions.append(Extension(
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+ "pysam.cvcf",
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+ cvcf_sources + os_c_files,
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+ library_dirs=[],
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+ include_dirs= ["lib/tabix",] + include_os,
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+ libraries=[ "z", ],
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+ language="c",
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+ ))
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return extensions
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