From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH]: Add HTSeq. Date: Fri, 20 Feb 2015 16:43:06 +0100 Message-ID: Mime-Version: 1.0 Content-Type: text/x-patch Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:38614) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YOpja-00049I-6I for guix-devel@gnu.org; Fri, 20 Feb 2015 10:43:19 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1YOpjW-00007d-RM for guix-devel@gnu.org; Fri, 20 Feb 2015 10:43:18 -0500 Received: from sinope.bbbm.mdc-berlin.de ([141.80.25.23]:53150) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YOpjW-00006z-HR for guix-devel@gnu.org; Fri, 20 Feb 2015 10:43:14 -0500 Received: from localhost (localhost [127.0.0.1]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP id ADBAC2807C1 for ; Fri, 20 Feb 2015 16:43:12 +0100 (CET) Received: from sinope.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id Ea888LWiAaMy for ; Fri, 20 Feb 2015 16:43:06 +0100 (CET) Received: from HTCATWO.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Fri, 20 Feb 2015 16:43:06 +0100 (CET) Content-Disposition: inline; filename="0001-gnu-Add-HTSeq.patch" 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 >From 3b812ce1c3458f832aa6eaac0d15502832bae8d5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 Feb 2015 16:41:50 +0100 Subject: [PATCH] gnu: Add HTSeq. * gnu/packages/bioinformatics.scm (htseq): New variable. --- gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c13e649..b64dab7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -311,6 +311,30 @@ several alignment strategies enable effective alignment of RNA-seq reads, in particular, reads spanning multiple exons.") (license license:gpl3+))) +(define-public htseq + (package + (name "htseq") + (version "0.6.1") + (source (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/H/HTSeq/HTSeq-" + version ".tar.gz")) + (sha256 + (base32 + "1i85ppf2j2lj12m0x690qq5nn17xxk23pbbx2c83r8ayb5wngzwv")))) + (build-system python-build-system) + (arguments `(#:python ,python-2)) ; only Python 2 is supported + (inputs + `(("python-numpy" ,python2-numpy) + ("python-setuptools" ,python2-setuptools))) + (home-page "http://www-huber.embl.de/users/anders/HTSeq/") + (synopsis "Analysing high-throughput sequencing data with Python") + (description + "HTSeq is a Python package that provides infrastructure to process data +from high-throughput sequencing assays.") + (license license:gpl3+))) + (define-public rseqc (package (name "rseqc") -- 2.1.0