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authorRicardo Wurmus <rekado@elephly.net>2018-10-21 12:51:31 +0200
committerRicardo Wurmus <rekado@elephly.net>2018-10-21 23:06:45 +0200
commit7321920cd3c9c1d7532024dfcdb958cce54b6368 (patch)
tree36f5343868db7148b90acfb2a24fe658a85966fd /gnu
parent8640f9ec91f7a9e81457a3651a06465fd8dd03a3 (diff)
downloadguix-7321920cd3c9c1d7532024dfcdb958cce54b6368.tar
guix-7321920cd3c9c1d7532024dfcdb958cce54b6368.tar.gz
gnu: crossmap: Update to 0.2.9.
* gnu/packages/bioinformatics.scm (crossmap): Update to 0.2.9. * gnu/packages/patches/crossmap-allow-system-pysam.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove patch.
Diffstat (limited to 'gnu')
-rw-r--r--gnu/local.mk1
-rw-r--r--gnu/packages/bioinformatics.scm25
-rw-r--r--gnu/packages/patches/crossmap-allow-system-pysam.patch121
3 files changed, 6 insertions, 141 deletions
diff --git a/gnu/local.mk b/gnu/local.mk
index c167e6753c..c76908f92f 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -634,7 +634,6 @@ dist_patch_DATA = \
%D%/packages/patches/cracklib-fix-buffer-overflow.patch \
%D%/packages/patches/crawl-upgrade-saves.patch \
%D%/packages/patches/crda-optional-gcrypt.patch \
- %D%/packages/patches/crossmap-allow-system-pysam.patch \
%D%/packages/patches/clucene-contribs-lib.patch \
%D%/packages/patches/cube-nocheck.patch \
%D%/packages/patches/cursynth-wave-rand.patch \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 795b0f208e..6469e9e1a1 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1894,31 +1894,18 @@ time.")
(define-public crossmap
(package
(name "crossmap")
- (version "0.2.1")
+ (version "0.2.9")
(source (origin
(method url-fetch)
- (uri (string-append "mirror://sourceforge/crossmap/CrossMap-"
- version ".tar.gz"))
+ (uri (pypi-uri "CrossMap" version))
(sha256
(base32
- "07y179f63d7qnzdvkqcziwk9bs3k4zhp81q392fp1hwszjdvy22f"))
- ;; This patch has been sent upstream already and is available
- ;; for download from Sourceforge, but it has not been merged.
- (patches (search-patches "crossmap-allow-system-pysam.patch"))
- (modules '((guix build utils)))
- (snippet '(begin
- ;; remove bundled copy of pysam
- (delete-file-recursively "lib/pysam")
- #t))))
+ "1byhclrqnqpvc1rqkfh4jwj6yhn0x9y7jk47i0qcjlhk0pjkw92p"))))
(build-system python-build-system)
- (arguments
- `(#:python ,python-2
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'set-env
- (lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1") #t)))))
+ (arguments `(#:python ,python-2))
(inputs
- `(("python-numpy" ,python2-numpy)
+ `(("python-bx-python" ,python2-bx-python)
+ ("python-numpy" ,python2-numpy)
("python-pysam" ,python2-pysam)
("zlib" ,zlib)))
(native-inputs
diff --git a/gnu/packages/patches/crossmap-allow-system-pysam.patch b/gnu/packages/patches/crossmap-allow-system-pysam.patch
deleted file mode 100644
index 611c4ff74d..0000000000
--- a/gnu/packages/patches/crossmap-allow-system-pysam.patch
+++ /dev/null
@@ -1,121 +0,0 @@
-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