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.
>From 63d3fe6a279489bb872708f30e1c74799e7702a5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus <[email protected]> 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
