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| author | Ben Woodcroft <donttrustben@gmail.com> | 2015-06-21 16:31:27 +1000 |
|---|---|---|
| committer | Mark H Weaver <mhw@netris.org> | 2015-06-21 03:30:40 -0400 |
| commit | 12b04cbee6b9c725db8a5c898b597de8e667bef0 (patch) | |
| tree | ed8e4bd5f76f1359e46e56473339d98db05aa10d | |
| parent | 407838510d39ee4b76160f5b553a3581b00f5c01 (diff) | |
| download | patches-12b04cbee6b9c725db8a5c898b597de8e667bef0.tar patches-12b04cbee6b9c725db8a5c898b597de8e667bef0.tar.gz | |
gnu: Add fasttree.
* gnu/packages/bioinformatics.scm (fasttree): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 59 |
1 files changed, 59 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 12c9175ed3..8dfaff3e00 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -780,6 +780,65 @@ analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data.") (license license:artistic2.0))) +(define-public fasttree + (package + (name "fasttree") + (version "2.1.8") + (source (origin + (method url-fetch) + (uri (string-append + "http://www.microbesonline.org/fasttree/FastTree-" + version ".c")) + (sha256 + (base32 + "0dzqc9vr9iiiw21y159xfjl2z90vw0y7r4x6456pcaxiy5hd2wmi")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no "check" target + #:phases + (modify-phases %standard-phases + (delete 'unpack) + (delete 'configure) + (replace 'build + (lambda* (#:key source #:allow-other-keys) + (and (zero? (system* "gcc" + "-O3" + "-finline-functions" + "-funroll-loops" + "-Wall" + "-o" + "FastTree" + source + "-lm")) + (zero? (system* "gcc" + "-DOPENMP" + "-fopenmp" + "-O3" + "-finline-functions" + "-funroll-loops" + "-Wall" + "-o" + "FastTreeMP" + source + "-lm"))))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") + "/bin"))) + (mkdir-p bin) + (copy-file "FastTree" + (string-append bin "/FastTree")) + (copy-file "FastTreeMP" + (string-append bin "/FastTreeMP")) + #t)))))) + (home-page "http://www.microbesonline.org/fasttree") + (synopsis "Infers approximately-maximum-likelihood phylogenetic trees") + (description + "FastTree can handle alignments with up to a million of sequences in a +reasonable amount of time and memory. For large alignments, FastTree is +100-1,000 times faster than PhyML 3.0 or RAxML 7.") + (license license:gpl2+))) + (define-public fastx-toolkit (package (name "fastx-toolkit") |