From 6e81c91c5e444cddf6e193f22d212b1eee3a5cab Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sat, 27 Jun 2015 09:29:23 +1000 Subject: [PATCH] gnu: Add prodigal. * gnu/packages/bioinformatics.scm (prodigal): New variable. --- gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 31df219..40a7d78 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1405,6 +1405,41 @@ files and writing bioinformatics applications.") generated using the PacBio Iso-Seq protocol.") (license license:bsd-3)))) +(define-public prodigal + (package + (name "prodigal") + (version "2.6.2") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/hyattpd/Prodigal/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0m8sb0fg6lmxrlpzna0am6svbnlmd3dckrhgzxxgb3gxr5fyj284")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ;no check target + #: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) + (copy-file "prodigal" (string-append bin "/prodigal")) + #t)))))) + (home-page "http://prodigal.ornl.gov") + (synopsis "Protein-coding gene prediction for Archaea and Bacteria") + (description + "Prodigal runs smoothly on finished genomes, draft genomes, and +metagenomes, providing gene predictions in GFF3, Genbank, or Sequin table +format. It runs quickly, in an unsupervised fashion, handles gaps, handles +partial genes, and identifies translation initiation sites.") + (license license:gpl3+))) + (define-public rsem (package (name "rsem") -- 2.4.3