From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] gnu: Add SEEK. Date: Wed, 15 Jun 2016 15:31:40 +0200 Message-ID: <20160615133140.13125-2-ricardo.wurmus@mdc-berlin.de> References: <20160615133140.13125-1-ricardo.wurmus@mdc-berlin.de> Mime-Version: 1.0 Content-Type: text/plain Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:57997) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bDAvu-00056L-Aw for guix-devel@gnu.org; Wed, 15 Jun 2016 09:32:39 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bDAvp-00067k-6w for guix-devel@gnu.org; Wed, 15 Jun 2016 09:32:38 -0400 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:53791) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bDAvo-00067X-RM for guix-devel@gnu.org; Wed, 15 Jun 2016 09:32:33 -0400 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id CE92A3807DD for ; Wed, 15 Jun 2016 15:32:31 +0200 (CEST) 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 1VfGt7BcNzjB for ; Wed, 15 Jun 2016 15:32:26 +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 venus.bbbm.mdc-berlin.de (Postfix) with ESMTPS for ; Wed, 15 Jun 2016 15:32:26 +0200 (CEST) In-Reply-To: <20160615133140.13125-1-ricardo.wurmus@mdc-berlin.de> 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" To: guix-devel@gnu.org * gnu/packages/bioinformatics.scm (seek): New variable. --- gnu/packages/bioinformatics.scm | 74 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 74 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d5f5500..71cf147 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -27,6 +27,7 @@ #:use-module (guix utils) #:use-module (guix download) #:use-module (guix git-download) + #:use-module (guix hg-download) #:use-module (guix build-system ant) #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) @@ -51,6 +52,7 @@ #:use-module (gnu packages gcc) #:use-module (gnu packages java) #:use-module (gnu packages linux) + #:use-module (gnu packages logging) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) @@ -61,6 +63,7 @@ #:use-module (gnu packages popt) #:use-module (gnu packages protobuf) #:use-module (gnu packages python) + #:use-module (gnu packages readline) #:use-module (gnu packages ruby) #:use-module (gnu packages statistics) #:use-module (gnu packages tbb) @@ -3145,6 +3148,77 @@ while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, etc.") (license license:gpl3+))) +(define-public seek + ;; There are no release tarballs. According to the installation + ;; instructions at http://seek.princeton.edu/installation.jsp, the latest + ;; stable release is identified by this changeset ID. + (let ((changeset "2329130") + (revision "1")) + (package + (name "seek") + (version (string-append "0-" revision "." changeset)) + (source (origin + (method hg-fetch) + (uri (hg-reference + (url "https://bitbucket.org/libsleipnir/sleipnir") + (changeset changeset))) + (sha256 + (base32 + "0qrvilwh18dpbhkf92qvxbmay0j75ra3jg2wrhz67gf538zzphsx")))) + (build-system gnu-build-system) + (arguments + `(#:modules ((srfi srfi-1) + (guix build gnu-build-system) + (guix build utils)) + #:phases + (let ((dirs '("SeekMiner" + "SeekEvaluator" + "SeekPrep" + "Distancer" + "Data2DB" + "PCL2Bin"))) + (modify-phases %standard-phases + (add-before 'configure 'bootstrap + (lambda _ + (zero? (system* "bash" "gen_auto")))) + (add-after 'build 'build-additional-tools + (lambda* (#:key make-flags #:allow-other-keys) + (fold (lambda (dir result) + (with-directory-excursion (string-append "tools/" dir) + (and result + (zero? (apply system* + `("make" ,@make-flags)))))) + #t dirs))) + (add-after 'install 'install-additional-tools + (lambda* (#:key make-flags #:allow-other-keys) + (fold (lambda (dir result) + (with-directory-excursion (string-append "tools/" dir) + (and result + (zero? (apply system* + `("make" ,@make-flags "install")))))) + #t dirs))))))) + (inputs + `(("gsl" ,gsl) + ("boost" ,boost) + ("libsvm" ,libsvm) + ("readline" ,readline) + ("gengetopt" ,gengetopt) + ("log4cpp" ,log4cpp))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("perl" ,perl))) + (home-page "http://seek.princeton.edu") + (synopsis "Gene co-expression search engine") + (description + "SEEK is a computational gene co-expression search engine. SEEK provides +biologists with a way to navigate the massive human expression compendium that +now contains thousands of expression datasets. SEEK returns a robust ranking +of co-expressed genes in the biological area of interest defined by the user's +query genes. It also prioritizes thousands of expression datasets according +to the user's query of interest.") + (license license:cc-by3.0)))) + (define-public samtools (package (name "samtools") -- 2.8.4