From mboxrd@z Thu Jan 1 00:00:00 1970 From: Roel Janssen Subject: [PATCH] gnu: Add bioawk. Date: Tue, 08 Mar 2016 21:10:14 +0100 Message-ID: <87d1r4eno9.fsf@gnu.org> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:54180) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1adNxS-0003CV-Js for guix-devel@gnu.org; Tue, 08 Mar 2016 15:10:19 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1adNxN-0005p3-PG for guix-devel@gnu.org; Tue, 08 Mar 2016 15:10:18 -0500 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:46900) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1adNxN-0005oq-Mc for guix-devel@gnu.org; Tue, 08 Mar 2016 15:10:13 -0500 Received: from 5469160b.cm-12-2a.dynamic.ziggo.nl ([84.105.22.11]:53058 helo=roel-tp) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_128_CBC_SHA1:128) (Exim 4.82) (envelope-from ) id 1adNxM-0005zR-TX for guix-devel@gnu.org; Tue, 08 Mar 2016 15:10:13 -0500 List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: guix-devel@gnu.org --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0001-gnu-Add-bioawk.patch >From 990eda92a62dc25d0f5792437a82e119c5e3579f Mon Sep 17 00:00:00 2001 From: Roel Janssen 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 --=-=-= Content-Type: text/plain 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 --=-=-=--