gnu: Add seqan.
* gnu/packages/bioinformatics.scm (seqan): New variable.
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@ -21,7 +21,9 @@
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#:use-module (guix packages)
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#:use-module (guix packages)
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#:use-module (guix download)
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#:use-module (guix download)
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#:use-module (guix build-system gnu)
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#:use-module (guix build-system gnu)
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#:use-module (guix build-system trivial)
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#:use-module (gnu packages)
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#:use-module (gnu packages)
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#:use-module (gnu packages base)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages ncurses)
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#:use-module (gnu packages ncurses)
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#:use-module (gnu packages perl)
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#:use-module (gnu packages perl)
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@ -198,3 +200,46 @@ sequence alignments in the SAM, BAM, and CRAM formats, including indexing,
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variant calling (in conjunction with bcftools), and a simple alignment
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variant calling (in conjunction with bcftools), and a simple alignment
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viewer.")
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viewer.")
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(license license:expat)))
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(license license:expat)))
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(define-public seqan
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(package
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(name "seqan")
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(version "1.4.2")
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(source (origin
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(method url-fetch)
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(uri (string-append "http://packages.seqan.de/seqan-library/"
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"seqan-library-" version ".tar.bz2"))
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(sha256
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(base32
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"05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp"))))
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;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it
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;; makes sense to split the outputs.
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(outputs '("out" "doc"))
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(build-system trivial-build-system)
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(arguments
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`(#:modules ((guix build utils))
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#:builder
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(begin
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(use-modules (guix build utils))
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(let ((tar (assoc-ref %build-inputs "tar"))
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(bzip (assoc-ref %build-inputs "bzip2"))
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(out (assoc-ref %outputs "out"))
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(doc (assoc-ref %outputs "doc")))
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(setenv "PATH" (string-append tar "/bin:" bzip "/bin"))
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(system* "tar" "xvf" (assoc-ref %build-inputs "source"))
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(chdir (string-append "seqan-library-" ,version))
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(copy-recursively "include" (string-append out "/include"))
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(copy-recursively "share" (string-append doc "/share"))))))
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(native-inputs
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`(("source" ,source)
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("tar" ,tar)
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("bzip2" ,bzip2)))
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(home-page "http://www.seqan.de")
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(synopsis "Library for nucleotide sequence analysis")
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(description
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"SeqAn is a C++ library of efficient algorithms and data structures for
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the analysis of sequences with the focus on biological data. It contains
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algorithms and data structures for string representation and their
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manipulation, online and indexed string search, efficient I/O of
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bioinformatics file formats, sequence alignment, and more.")
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(license license:bsd-3)))
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