Ben Woodcroft <address@hidden> skribis:
From acd310d27c457139d3f2fcd2cfc1127167bf2c48 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <address@hidden>
Date: Thu, 7 Jan 2016 07:44:58 +1000
Subject: [PATCH] gnu: Add fxtract.
* gnu/packages/bioinformatics.scm (fxtract): New variable.
[...]
+ `(("ctskennerton-util"
+ ,(origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ctSkennerton/util.git";)
+ (commit util-commit)))
This is GPLv2-only. Could you mention it in a comment?
+ (file-name (string-append
+ "ctstennerton-util-" util-commit "-checkout"))
I would make it:
(string-append "ctstennerton-util-" (string-take util-commit 7)
"-checkout")
+ (home-page "https://github.com/ctSkennerton/fxtract";)
+ (synopsis "Extract sequences from FASTA and FASTQ files")
+ (description
+ "Fxtract extracts sequences from a protein or nucleotide fastx (FASTA
+or FASTQ) file given a subsequence. It uses a simple substring search for
+basic tasks but can change to using POSIX regular expressions, PCRE, hash
+lookups or multi-pattern searching as required. By default fxtract looks in
+the sequence of each record but can also be told to look in the header,
+comment or quality sections.")
+ (license license:gpl3+))))
According to the ‘LICENSE’ file, this should be ‘license:expat’.
Otherwise LGTM.