A popular tool in microbial ecology.
>From ebec585b41d6a2bad6b9b04b07f0003ede389f1a Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrust...@gmail.com>
Date: Sat, 27 Jun 2015 09:24:08 +1000
Subject: [PATCH] gnu: Add prodigal.
* gnu/packages/bioinformatics.scm (prodigal): New variable.
---
gnu/packages/bioinformatics.scm | 34 ++++++++++++++++++++++++++++++++++
1 file changed, 34 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 31df219..8c6b010 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1405,6 +1405,40 @@ 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
