From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] Add MISO. Date: Fri, 13 Mar 2015 10:34:15 +0100 Message-ID: Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:53700) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YWLz9-0005sa-AA for guix-devel@gnu.org; Fri, 13 Mar 2015 05:34:33 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1YWLz5-00051D-Vk for guix-devel@gnu.org; Fri, 13 Mar 2015 05:34:27 -0400 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:54310) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YWLz5-000511-KG for guix-devel@gnu.org; Fri, 13 Mar 2015 05:34:23 -0400 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id C69413807B5 for ; Fri, 13 Mar 2015 10:34:21 +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 eH9qn-MwpKX6 for ; Fri, 13 Mar 2015 10:34:16 +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 ; Fri, 13 Mar 2015 10:34:16 +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 --=-=-= Content-Type: text/plain Hi Guix, the latest release of MISO corrected the license conflict (containing GPLv2 code but releasing the combined work under MIT) and is now released under the GPLv2. Attached is a patch to add MISO. ~~ Ricardo --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0001-gnu-Add-MISO.patch" >From aca149cc5c6c808535894b98d2f0b9ee96fe973c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 13 Mar 2015 10:31:49 +0100 Subject: [PATCH] gnu: Add MISO. * gnu/packages/bioinformatics.scm (miso): New variable. --- gnu/packages/bioinformatics.scm | 45 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 67326aa..faa3780 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -625,6 +625,51 @@ resolution of binding sites through combining the information of both sequencing tag position and orientation.") (license license:bsd-3))) +(define-public miso + (package + (name "miso") + (version "0.5.3") + (source (origin + (method url-fetch) + (uri (string-append + "http://pypi.python.org/packages/source/m/misopy/misopy-" + version ".tar.gz")) + (sha256 + (base32 + "0x446867az8ir0z8c1vjqffkp0ma37wm4sylixnkhgawllzx8v5w")) + (modules '((guix build utils))) + ;; use "gcc" instead of "cc" for compilation + (snippet + '(substitute* "setup.py" + (("^defines") + "cc.set_executables( +compiler='gcc', +compiler_so='gcc', +linker_exe='gcc', +linker_so='gcc -shared'); defines"))))) + (build-system python-build-system) + (arguments + `(#:python ,python-2 ; only Python 2 is supported + #:tests? #f)) ; no "test" target + (inputs + `(("samtools" ,samtools) + ("python-numpy" ,python2-numpy) + ("python-pysam" ,python2-pysam) + ("python-scipy" ,python2-scipy) + ("python-matplotlib" ,python2-matplotlib))) + (native-inputs + `(("python-setuptools" ,python2-setuptools))) + (home-page "http://genes.mit.edu/burgelab/miso/index.html") + (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation") + (description + "MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates +the expression level of alternatively spliced genes from RNA-Seq data, and +identifies differentially regulated isoforms or exons across samples. By +modeling the generative process by which reads are produced from isoforms in +RNA-Seq, the MISO model uses Bayesian inference to compute the probability +that a read originated from a particular isoform.") + (license license:gpl2))) + (define-public rseqc (package (name "rseqc") -- 2.1.0 --=-=-=--