From mboxrd@z Thu Jan 1 00:00:00 1970 From: Rob Syme Subject: [PATCH] gnu: Include CodingQuarry gene predictor Date: Tue, 8 Mar 2016 17:13:34 +0800 Message-ID: Mime-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:50257) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1adDiI-0004NK-R6 for guix-devel@gnu.org; Tue, 08 Mar 2016 04:14:00 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1adDiE-0002eU-RX for guix-devel@gnu.org; Tue, 08 Mar 2016 04:13:58 -0500 Received: from mail-ig0-x22a.google.com ([2607:f8b0:4001:c05::22a]:34855) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1adDiE-0002eM-NS for guix-devel@gnu.org; Tue, 08 Mar 2016 04:13:54 -0500 Received: by mail-ig0-x22a.google.com with SMTP id hb3so60403525igb.0 for ; Tue, 08 Mar 2016 01:13:54 -0800 (PST) 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/bioinformatics.scm: Add codingquarry package description --- gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5d53dc9..2e665db 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -914,6 +914,37 @@ also includes an interface for tabix.") "CLIPper is a tool to define peaks in CLIP-seq datasets.") (license license:gpl2))) +(define-public codingquarry + (package + (name "codingquarry") + (version "1.3") + (source (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/codingquarry/CodingQuarry_v" + version ".tar.gz")) + (sha256 + (base32 + "1nicv9k7g7w7c7zihr27xa27xnrd46p6n3b801hh13a7d5775fzi")))) + (build-system gnu-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'check) ;; Don't run the 'make check' step of the gnu-build-system + (replace 'install ;; Replace the install step with the function defined below + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (mkdir-p bin) + (copy-file "CodingQuarry" (string-append bin "/CodingQuarry")) + (copy-file "CufflinksGTF_to_CodingQuarryGFF3.py" (string-append bin "/CufflinksGTF_to_CodingQuarryGFF3.py")))))))) + (inputs `(("openmpi", openmpi))) + (native-inputs `(("python", python-2))) + (synopsis "CodingQuarry is a highly accurate, self-training GHMM fungal gene predictor") + (description "CodingQuarry is a highly accurate, self-training GHMM fungal gene predictor designed to work with assembled, aligned RNA-seq transcripts.") + (home-page "https://sourceforge.net/projects/codingquarry/") + (license licence:gpl3+))) + (define-public couger (package (name "couger") -- 2.5.0