From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] Add =?utf-8?Q?python=E2=80=93plastid=2C?= python-twobitreader. Date: Wed, 6 Apr 2016 16:36:52 +0200 Message-ID: Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:51586) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1anoZs-0005sB-Ir for guix-devel@gnu.org; Wed, 06 Apr 2016 10:37:05 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1anoZp-0000vt-C8 for guix-devel@gnu.org; Wed, 06 Apr 2016 10:37:04 -0400 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]:35876) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1anoZo-0000vp-VM for guix-devel@gnu.org; Wed, 06 Apr 2016 10:37:01 -0400 Received: from localhost (localhost [127.0.0.1]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 412B3380EDD for ; Wed, 6 Apr 2016 16:36:59 +0200 (CEST) Received: from pegasus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (pegasus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id qu1Emq9XsshV for ; Wed, 6 Apr 2016 16:36:53 +0200 (CEST) Received: from HTCATWO.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTPS for ; Wed, 6 Apr 2016 16:36:53 +0200 (CEST) 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 --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0001-gnu-Add-python-twobitreader.patch" >From ecb23f8eb2dbd83cbaa97972d6258ccb44c58194 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 6 Apr 2016 16:34:19 +0200 Subject: [PATCH 1/2] gnu: Add python-twobitreader. * gnu/packages/bioinformatics.scm (python-twobitreader, python2-twobitreader): New variables. --- gnu/packages/bioinformatics.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 01e9060..d13303d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1038,6 +1038,29 @@ also includes an interface for tabix.") (define-public python2-pysam (package-with-python2 python-pysam)) +(define-public python-twobitreader + (package + (name "python-twobitreader") + (version "3.1.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "twobitreader" version)) + (sha256 + (base32 + "0y408fp6psqzwxpcpqn0wp7fr41dwz8d54wpj6j261fj5q8vs169")))) + (build-system python-build-system) + (native-inputs + `(("python-sphinx" ,python-sphinx))) + (home-page "https://github.com/benjschiller/twobitreader") + (synopsis "Python library for reading .2bit files") + (description + "twobitreader is a Python library for reading .2bit files as used by the +UCSC genome browser.") + (license license:artistic2.0))) + +(define-public python2-twobitreader + (package-with-python2 python-twobitreader)) + (define-public cd-hit (package (name "cd-hit") -- 2.1.0 --=-=-= Content-Type: text/x-patch; charset="utf-8" Content-Disposition: inline; filename="0002-gnu-Add-python-plastid.patch" Content-Transfer-Encoding: quoted-printable >From a2604f6d4b03727ebd7922ce373486b13ab31c00 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 6 Apr 2016 16:35:09 +0200 Subject: [PATCH 2/2] gnu: Add python-plastid. * gnu/packages/bioinformatics.scm (python-plastid, python2-plastid): New variables. --- gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatic= s.scm index d13303d..1896002 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1061,6 +1061,41 @@ UCSC genome browser.") (define-public python2-twobitreader (package-with-python2 python-twobitreader)) =20 +(define-public python-plastid + (package + (name "python-plastid") + (version "0.4.5") + (source (origin + (method url-fetch) + (uri (pypi-uri "plastid" version)) + (sha256 + (base32 + "1nhxw8a5gn9as58i2ih52c5cjwj48ik418pzsjwph3s66mmy9yvq"))= )) + (build-system python-build-system) + (arguments + ;; Some test files are not included. + `(#:tests? #f)) + (propagated-inputs + `(("python-numpy" ,python-numpy) + ("python-scipy" ,python-scipy) + ("python-pandas" ,python-pandas) + ("python-pysam" ,python-pysam) + ("python-matplotlib" ,python-matplotlib) + ("python-biopython" ,python-biopython) + ("python-twobitreader" ,python-twobitreader))) + (native-inputs + `(("python-cython" ,python-cython) + ("python-nose" ,python-nose))) + (home-page "https://github.com/joshuagryphon/plastid") + (synopsis "Python library for genomic analysis") + (description + "plastid is a Python library for genomic analysis =E2=80=93 in part= icular, +high-throughput sequencing data =E2=80=93 with an emphasis on simplicity= .") + (license license:bsd-3))) + +(define-public python2-plastid + (package-with-python2 python-plastid)) + (define-public cd-hit (package (name "cd-hit") --=20 2.1.0 --=-=-=--