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| author | Ben Woodcroft <donttrustben@gmail.com> | 2015-10-15 22:53:31 +1000 |
|---|---|---|
| committer | Ludovic Courtès <ludo@gnu.org> | 2015-11-02 09:54:21 +0100 |
| commit | f3674b1c80a95d77be8aadea4575eb788cfac7cf (patch) | |
| tree | fb7cffc0ecd78a0c0a4254444cb80abfddf49730 | |
| parent | 6394fe650e7246dd0fcfb3f92a1797f7b6f3fcd1 (diff) | |
gnu: Add express-beta-diversity.
* gnu/packages/bioinformatics.scm (express-beta-diversity): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| -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 fdb42562e8..953684101d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1090,6 +1090,51 @@ analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data.") (license license:artistic2.0))) +(define-public express-beta-diversity + (package + (name "express-beta-diversity") + (version "1.0.7") + (source (origin + (method url-fetch) + (uri + (string-append + "https://github.com/dparks1134/ExpressBetaDiversity/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1djvdlmqvjf6h0zq7w36y8cl5cli6rgj86x65znl48agnwmzxfxr")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (delete 'configure) + (add-before 'build 'enter-source (lambda _ (chdir "source") #t)) + (replace 'check + (lambda _ (zero? (system* "../bin/ExpressBetaDiversity" + "-u")))) + (add-after 'check 'exit-source (lambda _ (chdir "..") #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") + "/bin"))) + (mkdir-p bin) + (copy-file "scripts/convertToEBD.py" + (string-append bin "/convertToEBD.py")) + (copy-file "bin/ExpressBetaDiversity" + (string-append bin "/ExpressBetaDiversity")) + #t)))))) + (inputs + `(("python" ,python-2))) + (home-page "http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity") + (synopsis "Taxon- and phylogenetic-based beta diversity measures") + (description + "Express Beta Diversity (EBD) calculates ecological beta diversity +(dissimilarity) measures between biological communities. EBD implements a +variety of diversity measures including those that make use of phylogenetic +similarity of community members.") + (license license:gpl3+))) + (define-public fasttree (package (name "fasttree") |