From be7134bf752c8223276f4f8ef12f67d52264474c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 23 Dec 2014 12:41:31 +0100
Subject: gnu: Add pysam.
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* gnu/packages/python.scm (python-pysam, python2-pysam): New variables.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/python.scm | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

(limited to 'gnu')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index f81ab695af..adb84fc5b7 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -37,6 +37,7 @@ (define-module (gnu packages python)
   #: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 @@ (define-public python-tzlocal
 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
-- 
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