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-rw-r--r--gnu/packages/bioinformatics.scm43
1 files changed, 43 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5d53dc9eef..b3d882761b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -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")