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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2014-12-23 12:41:31 +0100 |
|---|---|---|
| committer | Ludovic Courtès <ludo@gnu.org> | 2014-12-26 23:28:13 +0100 |
| commit | be7134bf752c8223276f4f8ef12f67d52264474c (patch) | |
| tree | 92c7d360e41a0aacd894cbb8e07f802dfb3968b6 /gnu | |
| parent | ee97be9fb46f869882390a2b491292ca0d44ce4d (diff) | |
| download | patches-be7134bf752c8223276f4f8ef12f67d52264474c.tar patches-be7134bf752c8223276f4f8ef12f67d52264474c.tar.gz | |
gnu: Add pysam.
* gnu/packages/python.scm (python-pysam, python2-pysam): New variables.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/python.scm | 38 |
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 |