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| author | Ricardo Wurmus <rekado@elephly.net> | 2019-03-20 11:58:35 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2019-03-20 12:19:55 +0100 |
| commit | 35f9c6628fd52adca03d08e503d65fa68c573a8e (patch) | |
| tree | 0b08f4fe5179b87e2fe41dc3db6a79ada1cafb1e /gnu | |
| parent | 7627bad6a7869b3f12b6659c326924f35a6fb28f (diff) | |
| download | gnu-guix-35f9c6628fd52adca03d08e503d65fa68c573a8e.tar gnu-guix-35f9c6628fd52adca03d08e503d65fa68c573a8e.tar.gz | |
gnu: Add adapterremoval.
* gnu/packages/bioinformatics.scm (adapterremoval): New variable.
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 37 |
1 files changed, 37 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index edfc651026..840ddfad17 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14602,3 +14602,40 @@ tools which build on STAR, Arriba does not require to reduce the ;; All code is under the Expat license with the exception of ;; "draw_fusions.R", which is under GPLv3. (license (list license:expat license:gpl3)))) + +(define-public adapterremoval + (package + (name "adapterremoval") + (version "2.3.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/MikkelSchubert/adapterremoval.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1nf3ki5pfzalhrx2fr1y6pfqfi133yj2m7q4fj9irf5fb94bapwr")))) + (build-system gnu-build-system) + (arguments + `(#:make-flags (list "COLOR_BUILD=no" + (string-append "PREFIX=" + (assoc-ref %outputs "out"))) + #:test-target "test" + #:phases + (modify-phases %standard-phases + (delete 'configure)))) + (inputs + `(("zlib" ,zlib))) + (home-page "https://adapterremoval.readthedocs.io/") + (synopsis "Rapid sequence adapter trimming, identification, and read merging") + (description + "This program searches for and removes remnant adapter sequences from +@dfn{High-Throughput Sequencing} (HTS) data and (optionally) trims low quality +bases from the 3' end of reads following adapter removal. AdapterRemoval can +analyze both single end and paired end data, and can be used to merge +overlapping paired-ended reads into (longer) consensus sequences. +Additionally, the AdapterRemoval may be used to recover a consensus adapter +sequence for paired-ended data, for which this information is not available.") + (license license:gpl3+))) |