From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:4830:134:3::10]:47140) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1dBEUj-0006bZ-FZ for guix-patches@gnu.org; Thu, 18 May 2017 02:01:06 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1dBEUg-0007Tz-CG for guix-patches@gnu.org; Thu, 18 May 2017 02:01:05 -0400 Received: from debbugs.gnu.org ([208.118.235.43]:49092) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1dBEUg-0007Tv-54 for guix-patches@gnu.org; Thu, 18 May 2017 02:01:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1dBEUf-0005N1-Ty for guix-patches@gnu.org; Thu, 18 May 2017 02:01:01 -0400 Subject: bug#26979: [PATCH] gnu: Add gemma. Resent-Message-ID: Received: from eggs.gnu.org ([2001:4830:134:3::10]:47099) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1dBEUH-0006ZR-FM for guix-patches@gnu.org; Thu, 18 May 2017 02:00:38 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1dBEUE-0007Qk-AW for guix-patches@gnu.org; Thu, 18 May 2017 02:00:37 -0400 Received: from mail.thebird.nl ([95.154.246.10]:46643) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1dBEUE-0007QF-51 for guix-patches@gnu.org; Thu, 18 May 2017 02:00:34 -0400 From: Pjotr Prins Date: Thu, 18 May 2017 05:59:47 +0000 Message-Id: <20170518055947.23560-1-pjotr.public12@thebird.nl> List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: 26979@debbugs.gnu.org Cc: Pjotr Prins From: Pjotr Prins * gnu/packages/bioinformatics.scm (gemma): New variable. --- gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9f5d8141d..d35b51d85 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2696,6 +2696,46 @@ comment or quality sections.") (supported-systems '("x86_64-linux")) (license license:expat)))) +(define-public gemma + (package + (name "gemma") + (version "0.96") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/xiangzhou/GEMMA/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "055ynn16gd12pf78n4vr2a9jlwsbwzajpdnf2y2yilg1krfff222")))) + (inputs + `(("gsl" ,gsl) + ("lapack" ,lapack) + ("zlib" ,zlib))) + (build-system gnu-build-system) + (arguments + `(#:make-flags '("FORCE_DYNAMIC=1") ; use shared libs + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-before 'build 'bin-mkdir + (lambda _ + (mkdir-p "bin"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (install-file "bin/gemma" + (string-append + out "/bin")))))) + #:tests? #f)) ; no tests included yet + (home-page "https://github.com/xiangzhou/GEMMA") + (synopsis "Tool for genome-wide efficient mixed model association") + (description + "Genome-wide Efficient Mixed Model Association (GEMMA) provides a +standard linear mixed model resolver with application in genome-wide +association studies (GWAS).") + (license license:gpl3))) + (define-public grit (package (name "grit") -- 2.11.0