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.
This commit is contained in:
Ricardo Wurmus
parent
1385d37a6e
commit
191c710139
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@ -375,6 +375,7 @@ dist_patch_DATA = \
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gnu/packages/patches/cpio-CVE-2014-9112-pt5.patch \
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gnu/packages/patches/cpio-CVE-2014-9112-pt5.patch \
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gnu/packages/patches/cpio-gets-undeclared.patch \
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gnu/packages/patches/cpio-gets-undeclared.patch \
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gnu/packages/patches/cpufrequtils-fix-aclocal.patch \
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gnu/packages/patches/cpufrequtils-fix-aclocal.patch \
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gnu/packages/patches/crossmap-allow-system-pysam.patch \
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gnu/packages/patches/cssc-gets-undeclared.patch \
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gnu/packages/patches/cssc-gets-undeclared.patch \
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gnu/packages/patches/cssc-missing-include.patch \
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gnu/packages/patches/cssc-missing-include.patch \
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gnu/packages/patches/clucene-contribs-lib.patch \
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gnu/packages/patches/clucene-contribs-lib.patch \
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@ -272,6 +272,48 @@ gapped, local, and paired-end alignment modes.")
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"CLIPper is a tool to define peaks in CLIP-seq datasets.")
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"CLIPper is a tool to define peaks in CLIP-seq datasets.")
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(license license:gpl2)))
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(license license:gpl2)))
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(define-public crossmap
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(package
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(name "crossmap")
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(version "0.1.6")
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(source (origin
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(method url-fetch)
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(uri (string-append "mirror://sourceforge/crossmap/CrossMap-"
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version ".tar.gz"))
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(sha256
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(base32
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"163hi5gjgij6cndxlvbkp5jjwr0k4wbm9im6d2210278q7k9kpnp"))
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;; patch has been sent upstream already
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(patches (list
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(search-patch "crossmap-allow-system-pysam.patch")))
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(modules '((guix build utils)))
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;; remove bundled copy of pysam
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(snippet
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'(delete-file-recursively "lib/pysam"))))
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(build-system python-build-system)
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(arguments
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`(#:python ,python-2
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#:phases
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(alist-cons-after
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'unpack 'set-env
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(lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1"))
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%standard-phases)))
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(inputs
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`(("python-numpy" ,python2-numpy)
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("python-pysam" ,python2-pysam)
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("zlib" ,zlib)))
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(native-inputs
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`(("python-cython" ,python2-cython)
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("python-nose" ,python2-nose)
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("python-setuptools" ,python2-setuptools)))
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(home-page "http://crossmap.sourceforge.net/")
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(synopsis "Convert genome coordinates between assemblies")
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(description
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"CrossMap is a program for conversion of genome coordinates or annotation
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files between different genome assemblies. It supports most commonly used
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file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
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(license license:gpl2+)))
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(define-public flexbar
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(define-public flexbar
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(package
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(package
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(name "flexbar")
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(name "flexbar")
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@ -0,0 +1,121 @@
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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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