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