From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
To: Guix-devel <guix-devel@gnu.org>
Subject: [PATCH] Add plink.
Date: Thu, 25 Jun 2015 12:05:29 +0200 [thread overview]
Message-ID: <idjegl0je6u.fsf@bimsb-sys02.mdc-berlin.net> (raw)
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Note: this is not PuTTY's plink, but a bioinformatics tool with the same
name.
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From d60d727bd9c2955c70ebf8cd3ee44becab64624e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
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
next reply other threads:[~2015-06-25 10:05 UTC|newest]
Thread overview: 3+ messages / expand[flat|nested] mbox.gz Atom feed top
2015-06-25 10:05 Ricardo Wurmus [this message]
2015-06-25 10:11 ` [PATCH] Add plink Ricardo Wurmus
2015-06-27 10:16 ` Ludovic Courtès
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