[PATCH]: gnu: Add seqan.

[PATCH]: gnu: Add seqan.

[Ricardo Wurmus]

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Attached is a patch that adds the seqan library to the bioinformatics
module.  Seqan is a header library, so it doesn't need to be built; it's
included in the build procedure of tools using it.

This package does not include the application bundle, which is really
just a number of applications by the same author depending on Seqan.

The documentation is 7.8MB and the includes are 3.6MB heavy, so I
decided to split the outputs.


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From 63d3fe6a279489bb872708f30e1c74799e7702a5 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 | 43 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 620c809..54c1a82 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -21,7 +21,9 @@
   #: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 +200,44 @@ sequence alignments in the SAM, BAM, and CRAM formats, including indexing,
 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"))))
+    (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 an open source 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)))
-- 
2.1.0

Re: [PATCH]: gnu: Add seqan.

[Ludovic Courtès]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:

> The documentation is 7.8MB and the includes are 3.6MB heavy, so I
> decided to split the outputs.

It’s a good idea to write it in a comment next to the ‘outputs’ field so
that passers-by know why it’s like this.

> From 63d3fe6a279489bb872708f30e1c74799e7702a5 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.

[...]

> +    (synopsis "Library for nucleotide sequence analysis")
> +    (description
> +     "SeqAn is an open source C++ library of efficient algorithms and data

s/open source//g

OK with these two changes.

Thank you!

Ludo’.