diff options
| author | Ben Woodcroft <donttrustben@gmail.com> | 2016-07-12 16:10:45 +1000 |
|---|---|---|
| committer | Ben Woodcroft <donttrustben@gmail.com> | 2016-08-08 22:08:17 +1000 |
| commit | 024130d2581b8dcdc0954b3c375afda29815806e (patch) | |
| tree | dfc17537dda4e36305663a141142d8615643ab22 | |
| parent | b16728b068ff9fda98b6f867a106a02bf5550364 (diff) | |
gnu: Add prank.
* gnu/packages/bioinformatics.scm (prank): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 52 |
1 files changed, 52 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 661bacb203..81431562f2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3259,6 +3259,58 @@ the phenotype as it models the data.") generated using the PacBio Iso-Seq protocol.") (license license:bsd-3)))) +(define-public prank + (package + (name "prank") + (version "150803") + (source (origin + (method url-fetch) + (uri (string-append + "http://wasabiapp.org/download/prank/prank.source." + version ".tgz")) + (sha256 + (base32 + "0am4z94fs3w2n5xpfls9zda61vq7qqz4q2i7b9hlsxz5q4j3kfm4")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'enter-src-dir + (lambda _ + (chdir "src") + #t)) + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (man (string-append out "/share/man/man1")) + (path (string-append + (assoc-ref %build-inputs "mafft") "/bin:" + (assoc-ref %build-inputs "exonerate") "/bin:" + (assoc-ref %build-inputs "bppsuite") "/bin"))) + (install-file "prank" bin) + (wrap-program (string-append bin "/prank") + `("PATH" ":" prefix (,path))) + (install-file "prank.1" man)) + #t))))) + (inputs + `(("mafft" ,mafft) + ("exonerate" ,exonerate) + ("bppsuite" ,bppsuite))) + (home-page "http://wasabiapp.org/software/prank/") + (synopsis "Probabilistic multiple sequence alignment program") + (description + "PRANK is a probabilistic multiple sequence alignment program for DNA, +codon and amino-acid sequences. It is based on a novel algorithm that treats +insertions correctly and avoids over-estimation of the number of deletion +events. In addition, PRANK borrows ideas from maximum likelihood methods used +in phylogenetics and correctly takes into account the evolutionary distances +between sequences. Lastly, PRANK allows for defining a potential structure +for sequences to be aligned and then, simultaneously with the alignment, +predicts the locations of structural units in the sequences.") + (license license:gpl2+))) + (define-public pyicoteo (package (name "pyicoteo") |