gnu: Add bioawk.

* gnu/packages/bioinformatics.scm (bioawk): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
This commit is contained in:
Roel Janssen 2016-03-10 23:54:31 +01:00 committed by Leo Famulari
parent 7bf4bd0991
commit a0a71439fa
1 changed files with 43 additions and 0 deletions

View File

@ -3,6 +3,7 @@
;;; Copyright © 2015, 2016 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -36,6 +37,7 @@
#:use-module (gnu packages autotools)
#:use-module (gnu packages algebra)
#:use-module (gnu packages base)
#:use-module (gnu packages bison)
#:use-module (gnu packages boost)
#:use-module (gnu packages compression)
#:use-module (gnu packages cpio)
@ -247,6 +249,47 @@ 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)
(inputs
`(("zlib" ,zlib)))
(native-inputs
`(("bison" ,bison)))
(arguments
`(#:tests? #f ; There are no tests to run.
;; Bison must generate files, before other targets can build.
#:parallel-build? #f
#:phases
(modify-phases %standard-phases
(delete 'configure) ; There is no configure phase.
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))
(man (string-append out "/share/man/man1")))
(mkdir-p man)
(copy-file "awk.1" (string-append man "/bioawk.1"))
(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 a 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")