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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2014-12-23 12:41:31 +0100
committerLudovic Courtès <ludo@gnu.org>2014-12-26 23:28:13 +0100
commitbe7134bf752c8223276f4f8ef12f67d52264474c (patch)
tree92c7d360e41a0aacd894cbb8e07f802dfb3968b6
parentee97be9fb46f869882390a2b491292ca0d44ce4d (diff)
downloadguix-be7134bf752c8223276f4f8ef12f67d52264474c.tar
guix-be7134bf752c8223276f4f8ef12f67d52264474c.tar.gz
gnu: Add pysam.
* gnu/packages/python.scm (python-pysam, python2-pysam): New variables. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
-rw-r--r--gnu/packages/python.scm38
1 files changed, 38 insertions, 0 deletions
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 @@
#: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