>From 990eda92a62dc25d0f5792437a82e119c5e3579f Mon Sep 17 00:00:00 2001
From: Roel Janssen <r...@gnu.org>
Date: Tue, 8 Mar 2016 21:06:53 +0100
Subject: [PATCH] gnu: Add bioawk.
* gnu/packages/bioinformatics.scm (bioawk): New variable.
---
gnu/packages/bioinformatics.scm | 38 ++++++++++++++++++++++++++++++++++++++
1 file changed, 38 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5d53dc9..4ceec08 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -37,6 +37,7 @@
#:use-module (gnu packages algebra)
#:use-module (gnu packages base)
#:use-module (gnu packages boost)
+ #:use-module (gnu packages bison)
#:use-module (gnu packages compression)
#:use-module (gnu packages cpio)
#:use-module (gnu packages curl)
@@ -247,6 +248,43 @@ intervals from multiple files in widely-used genomic file formats such as BAM,
BED, GFF/GTF, VCF.")
(license license:gpl2)))
+(define-public bioawk
+ (package
+ (name "bioawk")
+ (version "1.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/lh3/bioawk/archive/v";
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1daizxsk17ahi9n58fj8vpgwyhzrzh54bzqhanjanp88kgrz7gjw"))))
+ (build-system gnu-build-system)
+ (propagated-inputs
+ `(("zlib" ,zlib)))
+ (native-inputs
+ `(("bison" ,bison)))
+ (arguments
+ `(#:parallel-build? #f
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (delete 'check)
+ (replace
+ 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (install-file "bioawk" bin)))))))
+ (home-page "https://github.com/lh3/bioawk";)
+ (synopsis "AWK with bioinformatics extensions")
+ (description "Bioawk is an extension to Brian Kernighan's awk, adding the
+support of several common biological data formats, including optionally gzip'ed
+BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It
+also adds a few built-in functions and an command line option to use TAB as the
+input/output delimiter. When the new functionality is not used, bioawk is
+intended to behave exactly the same as the original BWK awk.")
+ (license license:x11)))
+
(define-public python2-pybedtools
(package
(name "python2-pybedtools")
--
2.5.0
Dear Guix,
Here's a patch to add bioawk -- a version of awk specialized in
biological data formats.
Please let me know when something is wrong with the patch.
Kind regards,
Roel Janssen
