From d3517eda25c74758ddedb04fa781aa65549248fe Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 6 Feb 2015 12:38:40 +0100
Subject: [PATCH] gnu: Add seqan.
* gnu/packages/bioinformatics.scm (seqan): New variable.
---
gnu/packages/bioinformatics.scm | 45 +++++++++++++++++++++++++++++++++
1 file changed, 45 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 620c8090b7c..0cae8274d5d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -21,7 +21,9 @@ (define-module (gnu packages bioinformatics)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix build-system gnu)
+ #:use-module (guix build-system trivial)
#:use-module (gnu packages)
+ #:use-module (gnu packages base)
#:use-module (gnu packages compression)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages perl)
@@ -198,3 +200,46 @@ (define-public samtools
variant calling (in conjunction with bcftools), and a simple alignment
viewer.")
(license license:expat)))
+
+(define-public seqan
+ (package
+ (name "seqan")
+ (version "1.4.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "http://packages.seqan.de/seqan-library/"
+ "seqan-library-" version ".tar.bz2"))
+ (sha256
+ (base32
+ "05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp"))))
+ ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it
+ ;; makes sense to split the outputs.
+ (outputs '("out" "doc"))
+ (build-system trivial-build-system)
+ (arguments
+ `(#:modules ((guix build utils))
+ #:builder
+ (begin
+ (use-modules (guix build utils))
+ (let ((tar (assoc-ref %build-inputs "tar"))
+ (bzip (assoc-ref %build-inputs "bzip2"))
+ (out (assoc-ref %outputs "out"))
+ (doc (assoc-ref %outputs "doc")))
+ (setenv "PATH" (string-append tar "/bin:" bzip "/bin"))
+ (system* "tar" "xvf" (assoc-ref %build-inputs "source"))
+ (chdir (string-append "seqan-library-" ,version))
+ (copy-recursively "include" (string-append out "/include"))
+ (copy-recursively "share" (string-append doc "/share"))))))
+ (native-inputs
+ `(("source" ,source)
+ ("tar" ,tar)
+ ("bzip2" ,bzip2)))
+ (home-page "http://www.seqan.de")
+ (synopsis "Library for nucleotide sequence analysis")
+ (description
+ "SeqAn is a C++ library of efficient algorithms and data structures for
+the analysis of sequences with the focus on biological data. It contains
+algorithms and data structures for string representation and their
+manipulation, online and indexed string search, efficient I/O of
+bioinformatics file formats, sequence alignment, and more.")
+ (license license:bsd-3)))
--
GitLab