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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2017-10-12 17:51:17 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2017-10-13 11:14:00 +0200 |
| commit | dc8ddbfb076e769d9a63d458e195c4705188bc0c (patch) | |
| tree | 4c9c00a4da14fc02305f50682250d0d09bdd9474 | |
| parent | f3eeca5621ac7c3644895e253395878dfdbdd87e (diff) | |
| download | guix-dc8ddbfb076e769d9a63d458e195c4705188bc0c.tar guix-dc8ddbfb076e769d9a63d458e195c4705188bc0c.tar.gz | |
gnu: Add paml.
* gnu/packages/bioinformatics.scm (paml): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 48 |
1 files changed, 48 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9a47b076c9..112d0e577c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10085,3 +10085,51 @@ straight away. Its main features are: and CHH context @end itemize\n") (license license:gpl3+))) + +(define-public paml + (package + (name "paml") + (version "4.9e") + (source (origin + (method url-fetch) + (uri (string-append "http://abacus.gene.ucl.ac.uk/software/" + "paml" version ".tgz")) + (sha256 + (base32 + "13zf6h9fiqghwhch2h06x1zdr6s42plsnqahflp5g7myr3han3s6")) + (modules '((guix build utils))) + ;; Remove Windows binaries + (snippet + '(begin + (for-each delete-file (find-files "." "\\.exe$")) + #t)))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; there are no tests + #:make-flags '("CC=gcc") + #:phases + (modify-phases %standard-phases + (replace 'configure + (lambda _ + (substitute* "src/BFdriver.c" + (("/bin/bash") (which "bash"))) + (chdir "src") + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((tools '("baseml" "basemlg" "codeml" + "pamp" "evolver" "yn00" "chi2")) + (bin (string-append (assoc-ref outputs "out") "/bin")) + (docdir (string-append (assoc-ref outputs "out") + "/share/doc/paml"))) + (mkdir-p bin) + (for-each (lambda (file) (install-file file bin)) tools) + (copy-recursively "../doc" docdir) + #t)))))) + (home-page "http://abacus.gene.ucl.ac.uk/software/paml.html") + (synopsis "Phylogentic analysis by maximum likelihood") + (description "PAML (for Phylogentic Analysis by Maximum Likelihood) +contains a few programs for model fitting and phylogenetic tree reconstruction +using nucleotide or amino-acid sequence data.") + ;; GPLv3 only + (license license:gpl3))) |