* [PATCH] Add vcftools.
@ 2015-03-20 15:53 Ricardo Wurmus
2015-03-24 21:01 ` Ludovic Courtès
0 siblings, 1 reply; 2+ messages in thread
From: Ricardo Wurmus @ 2015-03-20 15:53 UTC (permalink / raw)
To: guix-devel
[-- Attachment #1: Type: text/plain, Size: 136 bytes --]
Hi Guix,
Attached is a patch to add vcftools. The license of vcftools is
declared as LGPLv3.0 here[1] and in the README.
~~ Ricardo
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: 0001-gnu-Add-vcftools.patch --]
[-- Type: text/x-patch, Size: 2294 bytes --]
From 2f1b826719dbda30bfa63afbb7fd6457981258b3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 20 Mar 2015 16:50:33 +0100
Subject: [PATCH] gnu: Add vcftools.
* gnu/packages/bioinformatics.scm (vcftools): New variable.
---
gnu/packages/bioinformatics.scm | 38 ++++++++++++++++++++++++++++++++++++++
1 file changed, 38 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5805e42..a6e7e57 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1115,3 +1115,41 @@ combine multiple data representations, algorithm classes, and general purpose
tools. This enables both rapid prototyping of data pipelines and extensibility
in terms of new algorithms.")
(license license:gpl3+)))
+
+(define-public vcftools
+ (package
+ (name "vcftools")
+ (version "0.1.12b")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "mirror://sourceforge/vcftools/vcftools_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "148al9h7f8g8my2qdnpax51kdd2yjrivlx6frvakf4lz5r8j88wx"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; no "check" target
+ #:make-flags (list
+ (string-append "PREFIX=" (assoc-ref %outputs "out"))
+ (string-append "MANDIR=" (assoc-ref %outputs "out")
+ "/share/man/man1"))
+ #:phases
+ (alist-cons-after
+ 'unpack 'patch-manpage-install
+ (lambda _
+ (substitute* "Makefile"
+ (("cp \\$\\{PREFIX\\}/cpp/vcftools.1") "cp ./cpp/vcftools.1")))
+ (alist-delete 'configure %standard-phases))))
+ (inputs
+ `(("perl" ,perl)
+ ("zlib" ,zlib)))
+ (home-page "http://vcftools.sourceforge.net/")
+ (synopsis "Tools for working with VCF files")
+ (description
+ "VCFtools is a program package designed for working with VCF files, such
+as those generated by the 1000 Genomes Project. The aim of VCFtools is to
+provide easily accessible methods for working with complex genetic variation
+data in the form of VCF files.")
+ (license license:lgpl3)))
--
2.1.0
^ permalink raw reply related [flat|nested] 2+ messages in thread
* Re: [PATCH] Add vcftools.
2015-03-20 15:53 [PATCH] Add vcftools Ricardo Wurmus
@ 2015-03-24 21:01 ` Ludovic Courtès
0 siblings, 0 replies; 2+ messages in thread
From: Ludovic Courtès @ 2015-03-24 21:01 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
> Attached is a patch to add vcftools. The license of vcftools is
> declared as LGPLv3.0 here[1] and in the README.
Where’s the footnote? :-)
Anyway, it may be best to add this as a comment.
> From 2f1b826719dbda30bfa63afbb7fd6457981258b3 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Fri, 20 Mar 2015 16:50:33 +0100
> Subject: [PATCH] gnu: Add vcftools.
>
> * gnu/packages/bioinformatics.scm (vcftools): New variable.
LGTM!
Ludo’.
^ permalink raw reply [flat|nested] 2+ messages in thread
end of thread, other threads:[~2015-03-24 21:01 UTC | newest]
Thread overview: 2+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2015-03-20 15:53 [PATCH] Add vcftools Ricardo Wurmus
2015-03-24 21:01 ` Ludovic Courtès
Code repositories for project(s) associated with this public inbox
https://git.savannah.gnu.org/cgit/guix.git
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).