From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: [PATCH] gnu: Add seqtk. Date: Fri, 9 Sep 2016 21:08:34 +1000 Message-ID: <20160909110834.8581-1-donttrustben@gmail.com> References: <20150718090748.GA26418@jocasta.intra> Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:57400) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1biJfv-0001ZL-07 for guix-devel@gnu.org; Fri, 09 Sep 2016 07:08:52 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1biJfq-0008Q7-Qe for guix-devel@gnu.org; Fri, 09 Sep 2016 07:08:50 -0400 Received: from mail-pf0-x243.google.com ([2607:f8b0:400e:c00::243]:36149) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1biJfq-0008Pw-Ir for guix-devel@gnu.org; Fri, 09 Sep 2016 07:08:46 -0400 Received: by mail-pf0-x243.google.com with SMTP id x24so3883005pfa.3 for ; Fri, 09 Sep 2016 04:08:46 -0700 (PDT) In-Reply-To: <20150718090748.GA26418@jocasta.intra> 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" To: guix-devel@gnu.org From: Ben J Woodcroft Well, despite the lightness of my touch, it seems the licensing is in now in order. I've updated the package, here's an updated patch. Better? Thanks, ben * gnu/packages/bioinformatics.scm (seqtk): New variable. --- gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f34acd1..4e296f5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4529,6 +4529,41 @@ BioPython in a convenient way. Instead of having a big mess of scripts, there is one that takes arguments.") (license license:gpl3))) +(define-public seqtk + (package + (name "seqtk") + (version "1.2") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/lh3/seqtk/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0ywdyzpmfiz2wp6ampbzqg4y8bj450nfgqarpamg045b8mk32lxx")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'check + ;; There are no tests, so we just run a sanity check. + (lambda _ (zero? (system* "./seqtk" "seq")))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) + (install-file "seqtk" bin))))))) + (inputs + `(("zlib" ,zlib))) + (home-page "https://github.com/lh3/seqtk") + (synopsis "Toolkit for biological sequences in FASTA/Q formats") + (description + "Seqtk is a fast and lightweight tool for processing sequences in the +FASTA or FASTQ format. It parses both FASTA and FASTQ files which can be +optionally compressed by gzip.") + (license license:expat))) + (define-public snap-aligner (package (name "snap-aligner") -- 2.9.1