diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 43 |
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") |