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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-10-16 17:41:07 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-10-22 11:11:09 +0200 |
| commit | fe4c37c244c0fb786c135e2da62306dc90df5638 (patch) | |
| tree | e2e4864dab950c7ecbade1c760c9e5d776dfb8f6 | |
| parent | 1e656049b01bdeb2370229641ef8e0def92b4f89 (diff) | |
| download | patches-fe4c37c244c0fb786c135e2da62306dc90df5638.tar patches-fe4c37c244c0fb786c135e2da62306dc90df5638.tar.gz | |
gnu: Add MOSAIK.
* gnu/packages/bioinformatics.scm (mosaik): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 46 |
1 files changed, 46 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 51e3df6d81..48edd56854 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2149,6 +2149,52 @@ viewer.") (string-append bin "/samtools"))))) (delete 'patch-tests))))))) +(define-public mosaik + (let ((commit "5c25216d")) + (package + (name "mosaik") + (version "2.2.30") + (source (origin + ;; There are no release tarballs nor tags. + (method git-fetch) + (uri (git-reference + (url "https://github.com/wanpinglee/MOSAIK.git") + (commit commit))) + (file-name (string-append name "-" version)) + (sha256 + (base32 + "17gj3s07cm77r41z92awh0bim7w7q7fbn0sf5nkqmcm1vw052qgw")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no tests + #:make-flags (list "CC=gcc") + #:phases + (modify-phases %standard-phases + (replace 'configure + (lambda _ (chdir "src") #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") + "/bin"))) + (mkdir-p bin) + (copy-recursively "../bin" bin) + #t)))))) + (inputs + `(("perl" ,perl) + ("zlib" ,zlib))) + (home-page "https://code.google.com/p/mosaik-aligner/") + (synopsis "Map nucleotide sequence reads to reference genomes") + (description + "MOSAIK is a program for mapping second and third-generation sequencing +reads to a reference genome. MOSAIK can align reads generated by all the +major sequencing technologies, including Illumina, Applied Biosystems SOLiD, +Roche 454, Ion Torrent and Pacific BioSciences SMRT.") + ;; MOSAIK is released under the GPLv2+ with the exception of third-party + ;; code released into the public domain: + ;; 1. fastlz by Ariya Hidayat - http://www.fastlz.org/ + ;; 2. MD5 implementation - RSA Data Security, RFC 1321 + (license (list license:gpl2+ license:public-domain))))) + (define-public ngs-sdk (package (name "ngs-sdk") |