From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] gnu: Add pysam Date: Tue, 23 Dec 2014 12:41:31 +0100 Message-ID: Mime-Version: 1.0 Content-Type: text/plain Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:38421) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Y3NsN-0008BT-CF for guix-devel@gnu.org; Tue, 23 Dec 2014 06:43:48 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Y3NsI-0007u4-0w for guix-devel@gnu.org; Tue, 23 Dec 2014 06:43:43 -0500 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:36640) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Y3NsH-0007tl-OS for guix-devel@gnu.org; Tue, 23 Dec 2014 06:43:37 -0500 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 0F9F03804BD for ; Tue, 23 Dec 2014 12:43:36 +0100 (CET) Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id OPyG65c3NdFX for ; Tue, 23 Dec 2014 12:43:30 +0100 (CET) Received: from HTCATWO.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Tue, 23 Dec 2014 12:43:30 +0100 (CET) List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: guix-devel@gnu.org * 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