* [PATCH] gnu: Add pysam
@ 2014-12-23 11:41 Ricardo Wurmus
2014-12-26 22:08 ` Ludovic Courtès
0 siblings, 1 reply; 2+ messages in thread
From: Ricardo Wurmus @ 2014-12-23 11:41 UTC (permalink / raw)
To: guix-devel
* gnu/packages/python.scm (python-pysam, python2-pysam): New variables.
---
gnu/packages/python.scm | 38 ++++++++++++++++++++++++++++++++++++++
1 file changed, 38 insertions(+)
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index f81ab69..24bec00 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -37,6 +37,7 @@
#:use-module (gnu packages openssl)
#:use-module (gnu packages elf)
#:use-module (gnu packages maths)
+ #:use-module (gnu packages ncurses)
#:use-module (gnu packages gcc)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages databases)
@@ -617,6 +618,43 @@ get the local timezone information, unless you know the zoneinfo name, and
under several distributions that's hard or impossible to figure out.")
(license cc0)))
+(define-public python-pysam
+ (package
+ (name "python-pysam")
+ (version "0.8.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://pypi.python.org/packages/source/p/pysam/pysam-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1fb6i6hbpzxaxb62kyyp5alaidwhj40f7c6gwbhr6njzlqd5l459"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:tests? #f ; tests are excluded in the manifest
+ #:phases
+ (alist-cons-before
+ 'build 'set-flags
+ (lambda _
+ (setenv "LDFLAGS" "-lncurses")
+ (setenv "CFLAGS" "-D_CURSES_LIB=1"))
+ %standard-phases)))
+ (inputs
+ `(("python-cython" ,python-cython)
+ ("python-setuptools" ,python-setuptools)
+ ("ncurses" ,ncurses)
+ ("zlib" ,zlib)))
+ (home-page "https://github.com/pysam-developers/pysam")
+ (synopsis "Python bindings to the samtools C-API")
+ (description
+ "Pysam is a python module for reading and manipulating files in the
+SAM/BAM format. Pysam is a lightweight wrapper of the samtools C-API. It
+also includes an interface for tabix.")
+ (license expat)))
+
+(define-public python2-pysam
+ (package-with-python2 python-pysam))
(define-public python2-pysqlite
(package
--
1.9.3
^ permalink raw reply related [flat|nested] 2+ messages in thread
* Re: [PATCH] gnu: Add pysam
2014-12-23 11:41 [PATCH] gnu: Add pysam Ricardo Wurmus
@ 2014-12-26 22:08 ` Ludovic Courtès
0 siblings, 0 replies; 2+ messages in thread
From: Ludovic Courtès @ 2014-12-26 22:08 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
> * gnu/packages/python.scm (python-pysam, python2-pysam): New variables.
Applied, thanks!
Ludo’.
^ permalink raw reply [flat|nested] 2+ messages in thread
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2014-12-26 22:08 ` Ludovic Courtès
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