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.

gnu-system.am

@@ -375,6 +375,7 @@ dist_patch_DATA =						\
   gnu/packages/patches/cpio-CVE-2014-9112-pt5.patch		\
   gnu/packages/patches/cpio-gets-undeclared.patch		\
   gnu/packages/patches/cpufrequtils-fix-aclocal.patch		\
+  gnu/packages/patches/crossmap-allow-system-pysam.patch	\
   gnu/packages/patches/cssc-gets-undeclared.patch               \
   gnu/packages/patches/cssc-missing-include.patch               \
   gnu/packages/patches/clucene-contribs-lib.patch               \

gnu/packages/bioinformatics.scm

@@ -272,6 +272,48 @@ (define-public clipper
      "CLIPper is a tool to define peaks in CLIP-seq datasets.")
     (license license:gpl2)))
 
+(define-public crossmap
+  (package
+    (name "crossmap")
+    (version "0.1.6")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/crossmap/CrossMap-"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "163hi5gjgij6cndxlvbkp5jjwr0k4wbm9im6d2210278q7k9kpnp"))
+              ;; patch has been sent upstream already
+              (patches (list
+                        (search-patch "crossmap-allow-system-pysam.patch")))
+              (modules '((guix build utils)))
+              ;; remove bundled copy of pysam
+              (snippet
+               '(delete-file-recursively "lib/pysam"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2
+       #:phases
+       (alist-cons-after
+        'unpack 'set-env
+        (lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1"))
+        %standard-phases)))
+    (inputs
+     `(("python-numpy" ,python2-numpy)
+       ("python-pysam" ,python2-pysam)
+       ("zlib" ,zlib)))
+    (native-inputs
+     `(("python-cython" ,python2-cython)
+       ("python-nose" ,python2-nose)
+       ("python-setuptools" ,python2-setuptools)))
+    (home-page "http://crossmap.sourceforge.net/")
+    (synopsis "Convert genome coordinates between assemblies")
+    (description
+     "CrossMap is a program for conversion of genome coordinates or annotation
+files between different genome assemblies.  It supports most commonly used
+file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
+    (license license:gpl2+)))
+
 (define-public flexbar
   (package
     (name "flexbar")

gnu/packages/patches/crossmap-allow-system-pysam.patch

+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