[PATCH] gnu: Add pysam

[PATCH] gnu: Add pysam

[Ricardo Wurmus]

* 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

Re: [PATCH] gnu: Add pysam

[Ludovic Courtès]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:

> * gnu/packages/python.scm (python-pysam, python2-pysam): New variables.

Applied, thanks!

Ludo’.