06/28: gnu: crossmap: Update to 0.2.9.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit 7321920cd3c9c1d7532024dfcdb958cce54b6368
Author: Ricardo Wurmus <address@hidden>
Date:   Sun Oct 21 12:51:31 2018 +0200

    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.
---
 gnu/local.mk                                       |   1 -
 gnu/packages/bioinformatics.scm                    |  25 +----
 .../patches/crossmap-allow-system-pysam.patch      | 121 ---------------------
 3 files changed, 6 insertions(+), 141 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index c167e67..c76908f 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 795b0f2..6469e9e 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 611c4ff..0000000
--- 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