On 27/06/15 20:40, Ricardo Wurmus wrote:
+ (synopsis "Protein-coding gene prediction for Archaea and Bacteria")
Shouldn’t “Archaea” and “Bacteria” both be lower-cased?
I don't believe so. As I understand it you can use "bacterial" and
"archaeal" with lower case, but here we are referring to the domains as
nouns.
I did take some small liberties here. The original sentence on the web was
>Fast, reliable protein-coding gene prediction for prokaryotic genomes.
To me this is problematic in two ways:
1. It works on more than just genomes
2. There is some contention in the field about the use of "prokaryote",
since this refers to a paraphyletic group - us humans are more closely
related to Archaea than Bacteria.
http://link.springer.com/referenceworkentry/10.1007/978-3-642-30194-0_114
I figure it was just easier to sidestep the issue and put Archaea and
Bacteria.
another thing just occurred to me. Instead of replacing the install
phase you might just overwrite the INSTALLDIR variable, something like
this:
#:make-flags (list (string-append "INSTALLDIR="
(assoc-ref %outputs "out")))
What do you think?
That made it more concise, and maybe more future proof (though need
added "/bin").
>From 086a910d53995cb209a7413c74705d2ad3b8e17e Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrust...@gmail.com>
Date: Sat, 27 Jun 2015 22:28:19 +1000
Subject: [PATCH] gnu: Add prodigal.
* gnu/packages/bioinformatics.scm (prodigal): New variable.
---
gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++
1 file changed, 31 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 31df219..f321d82 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1405,6 +1405,37 @@ 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
+ #:make-flags (list (string-append "INSTALLDIR="
+ (assoc-ref %outputs "out")
+ "/bin"))
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure))))
+ (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
