From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] Add plink. Date: Thu, 25 Jun 2015 12:05:29 +0200 Message-ID: Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:41932) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z842W-0006rN-46 for guix-devel@gnu.org; Thu, 25 Jun 2015 06:05:52 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Z842R-0005FQ-3n for guix-devel@gnu.org; Thu, 25 Jun 2015 06:05:48 -0400 Received: from sinope.bbbm.mdc-berlin.de ([141.80.25.23]:39360) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z842Q-0005Bz-NH for guix-devel@gnu.org; Thu, 25 Jun 2015 06:05:43 -0400 Received: from localhost (localhost [127.0.0.1]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP id E886A280748 for ; Thu, 25 Jun 2015 12:05:36 +0200 (CEST) Received: from sinope.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id j_UpW1o4gDMI for ; Thu, 25 Jun 2015 12:05:30 +0200 (CEST) Received: from HTCAONE.mdc-berlin.net (mab.citx.mdc-berlin.de [141.80.36.102]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Thu, 25 Jun 2015 12:05:30 +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/plain Note: this is not PuTTY's plink, but a bioinformatics tool with the same name. --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0001-gnu-Add-plink.patch" >From d60d727bd9c2955c70ebf8cd3ee44becab64624e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 25 Jun 2015 12:04:05 +0200 Subject: [PATCH] gnu: Add plink. * gnu/packages/bioinformatics.scm (plink): New variable. --- gnu/packages/bioinformatics.scm | 53 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7e94bf3..a4bb303 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2033,6 +2033,59 @@ Databases are stored in a portable image within the file system, and can be accessed/downloaded on demand across HTTP.") (license license:public-domain))) +(define-public plink + (package + (name "plink") + (version "1.07") + (source + (origin + (method url-fetch) + (uri (string-append + "http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-" + version "-src.zip")) + (sha256 + (base32 "0as8gxm4pjyc8dxmm1sl873rrd7wn5qs0l29nqfnl31x8i467xaa")) + (patches (list (search-patch "plink-1.07-unclobber-i.patch"))))) + (build-system gnu-build-system) + (arguments + '(#:tests? #f ;no "check" target + #:make-flags (list (string-append "LIB_LAPACK=" + (assoc-ref %build-inputs "lapack") + "/lib/liblapack.so") + "WITH_LAPACK=1" + "FORCE_DYNAMIC=1" + ;; disable phoning home + "WITH_WEBCHECK=") + #:phases + (modify-phases %standard-phases + ;; no "configure" script + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") + "/bin/"))) + (mkdir-p bin) + (copy-file "plink" (string-append bin "plink")) + #t)))))) + (inputs + `(("zlib" ,zlib) + ("lapack" ,lapack))) + (native-inputs + `(("unzip" ,unzip))) + (home-page "http://pngu.mgh.harvard.edu/~purcell/plink/") + (synopsis "Whole genome association analysis toolset") + (description + "PLINK is a whole genome association analysis toolset, designed to +perform a range of basic, large-scale analyses in a computationally efficient +manner. The focus of PLINK is purely on analysis of genotype/phenotype data, +so there is no support for steps prior to this (e.g. study design and +planning, generating genotype or CNV calls from raw data). Through +integration with gPLINK and Haploview, there is some support for the +subsequent visualization, annotation and storage of results.") + ;; Code is released under GPLv2, except for fisher.h, which is under + ;; LGPLv2.1+ + (license (list license:gpl2 license:lgpl2.1+)))) + (define-public preseq (package (name "preseq") -- 2.1.0 --=-=-=--