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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2016-05-20 16:09:59 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2016-05-23 12:55:09 +0200 |
| commit | 078378743698f71e4b43dffa5627c86d3ebccc29 (patch) | |
| tree | 0027d8a3c6acbf07a241769d32606667f37c32dd /gnu/packages/bioinformatics.scm | |
| parent | 624d4e2e6ba402c374a340869306eec65a808a20 (diff) | |
| download | patches-078378743698f71e4b43dffa5627c86d3ebccc29.tar patches-078378743698f71e4b43dffa5627c86d3ebccc29.tar.gz | |
gnu: Add ParDRe.
* gnu/packages/bioinformatics.scm (pardre): New variable.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 41 |
1 files changed, 41 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d404ff839c..dae162ef0b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3885,6 +3885,47 @@ Needleman-Wunsch).") ;; Dual licensed; also includes public domain source. (license (list license:gpl3 license:bsd-2)))) +(define-public pardre + (package + (name "pardre") + (version "1.1.5") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/pardre/ParDRe-rel" + version ".tar.gz")) + (sha256 + (base32 + "0zkyjzv4s8q2h5npalhirbk17r5b1h0n2a42mh7njzlf047h9bhy")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no tests included + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (mkdir-p bin) + (install-file "ParDRe" bin) + #t)))))) + (inputs + `(("openmpi" ,openmpi) + ("zlib" ,zlib))) + (synopsis "Parallel tool to remove duplicate DNA reads") + (description + "ParDRe is a parallel tool to remove duplicate genetic sequence reads. +Duplicate reads can be seen as identical or nearly identical sequences with +some mismatches. This tool lets users avoid the analysis of unnecessary +reads, reducing the time of subsequent procedures with the +dataset (e.g. assemblies, mappings, etc.). The tool is implemented with MPI +in order to exploit the parallel capabilities of multicore clusters. It is +faster than multithreaded counterparts (end of 2015) for the same number of +cores and, thanks to the message-passing technology, it can be executed on +clusters.") + (home-page "https://sourceforge.net/projects/pardre/") + (license license:gpl3+))) + (define-public bio-locus (package (name "bio-locus") |