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01/01: gnu: Add crossmap.
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From: |
Ricardo Wurmus |
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Subject: |
01/01: gnu: Add crossmap. |
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Date: |
Mon, 02 Mar 2015 16:24:04 +0000 |
rekado pushed a commit to branch master
in repository guix.
commit 191c710139af3e833f32b24ce1f225c344620bb3
Author: Ricardo Wurmus <address@hidden>
Date: Thu Feb 26 16:34:49 2015 +0100
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 | 1 +
gnu/packages/bioinformatics.scm | 42 +++++++
.../patches/crossmap-allow-system-pysam.patch | 121 ++++++++++++++++++++
3 files changed, 164 insertions(+), 0 deletions(-)
diff --git a/gnu-system.am b/gnu-system.am
index e42e89a..a500ec7 100644
--- a/gnu-system.am
+++ b/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 \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index de25f8c..0960329 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -272,6 +272,48 @@ gapped, local, and paired-end alignment modes.")
"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")
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 0000000..611c4ff
--- /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