From 191c710139af3e833f32b24ce1f225c344620bb3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 26 Feb 2015 16:34:49 +0100
Subject: gnu: Add crossmap.

* 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.
---
 .../patches/crossmap-allow-system-pysam.patch      | 121 +++++++++++++++++++++
 1 file changed, 121 insertions(+)
 create mode 100644 gnu/packages/patches/crossmap-allow-system-pysam.patch

(limited to 'gnu/packages/patches')

diff --git a/gnu/packages/patches/crossmap-allow-system-pysam.patch b/gnu/packages/patches/crossmap-allow-system-pysam.patch
new file mode 100644
index 0000000000..611c4ff74d
--- /dev/null
+++ b/gnu/packages/patches/crossmap-allow-system-pysam.patch
@@ -0,0 +1,121 @@
+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     
-- 
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