From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
To: Guix-devel <guix-devel@gnu.org>
Subject: [PATCH] gnu: Add crossmap.
Date: Thu, 26 Feb 2015 16:38:02 +0100 [thread overview]
Message-ID: <idj4mq8heed.fsf@bimsb-sys02.mdc-berlin.net> (raw)
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #1: 0001-gnu-Add-crossmap.patch --]
[-- Type: text/x-patch, Size: 7821 bytes --]
From e93da9b48bafbbfa56fe348cabad9e074eda63fb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 26 Feb 2015 16:34:49 +0100
Subject: [PATCH] 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 | 113 +++++++++++++++++++++
3 files changed, 156 insertions(+)
create mode 100644 gnu/packages/patches/crossmap-allow-system-pysam.patch
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 1103d92..749d0a0 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..a16f901
--- /dev/null
+++ b/gnu/packages/patches/crossmap-allow-system-pysam.patch
@@ -0,0 +1,113 @@
+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
--
2.1.0
next reply other threads:[~2015-02-26 15:38 UTC|newest]
Thread overview: 2+ messages / expand[flat|nested] mbox.gz Atom feed top
2015-02-26 15:38 Ricardo Wurmus [this message]
2015-02-28 14:53 ` [PATCH] gnu: Add crossmap Ludovic Courtès
Reply instructions:
You may reply publicly to this message via plain-text email
using any one of the following methods:
* Save the following mbox file, import it into your mail client,
and reply-to-all from there: mbox
Avoid top-posting and favor interleaved quoting:
https://en.wikipedia.org/wiki/Posting_style#Interleaved_style
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to=idj4mq8heed.fsf@bimsb-sys02.mdc-berlin.net \
--to=ricardo.wurmus@mdc-berlin.de \
--cc=guix-devel@gnu.org \
/path/to/YOUR_REPLY
https://kernel.org/pub/software/scm/git/docs/git-send-email.html
* If your mail client supports setting the In-Reply-To header
via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line
before the message body.
Code repositories for project(s) associated with this external index
https://git.savannah.gnu.org/cgit/guix.git
This is an external index of several public inboxes,
see mirroring instructions on how to clone and mirror
all data and code used by this external index.