diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 45 |
1 files changed, 45 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 620c8090b7..0cae8274d5 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 +200,46 @@ 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")))) + ;; 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))) |