From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: [PATCH 3/4] gnu: Add barrnap. Date: Sat, 3 Dec 2016 20:39:00 +1000 Message-ID: <20161203103901.27770-3-donttrustben@gmail.com> References: <20161203103901.27770-1-donttrustben@gmail.com> Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:50359) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cD7j0-0000q2-Vv for guix-devel@gnu.org; Sat, 03 Dec 2016 05:39:24 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cD7iz-0006Ae-SU for guix-devel@gnu.org; Sat, 03 Dec 2016 05:39:23 -0500 Received: from mail-pf0-x242.google.com ([2607:f8b0:400e:c00::242]:32885) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1cD7iz-0006AJ-KE for guix-devel@gnu.org; Sat, 03 Dec 2016 05:39:21 -0500 Received: by mail-pf0-x242.google.com with SMTP id 144so14870938pfv.0 for ; Sat, 03 Dec 2016 02:39:21 -0800 (PST) Received: from localhost.localdomain ([103.25.181.216]) by smtp.googlemail.com with ESMTPSA id o68sm13952132pfb.42.2016.12.03.02.39.16 for (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Sat, 03 Dec 2016 02:39:18 -0800 (PST) In-Reply-To: <20161203103901.27770-1-donttrustben@gmail.com> 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 * gnu/packages/bioinformatics.scm (barrnap): New variable. --- gnu/packages/bioinformatics.scm | 67 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 67 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 961f0b2..4541791 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -268,6 +268,73 @@ instance, it implements several methods to assess contig-wise read coverage.") BAM files.") (license license:expat))) +(define-public barrnap + (package + (name "barrnap") + (version "0.7") + (source + (origin + (method url-fetch) + (uri (string-append + "https://github.com/tseemann/barrnap/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "16y040np76my3y82hgk4yy790smbsk4h8d60d5swlv7ha3i768gg")) + (modules '((guix build utils))) + ;; Remove pre-built binaries. + (snippet '(begin + (delete-file-recursively "binaries") + #t)))) + (build-system gnu-build-system) + (arguments + `(#:test-target "test" + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-nhmer-path + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "bin/barrnap" + (("^my \\$NHMMER = .*") + (string-append "my $NHMMER = '" + (assoc-ref inputs "hmmer") + "/bin/nhmmer';\n"))) + #t)) + (delete 'configure) + (delete 'build) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + ;(path (getenv "PATH")) + (share (string-append out "/share/barrnap/db")) + (binary "bin/barrnap")) + (substitute* binary + (("^my \\$DBDIR = .*") + (string-append "my $DBDIR = '" share "';\n"))) + (install-file binary bin) + (mkdir-p share) + (copy-recursively "db" share)) + #t))))) + (inputs + `(("perl" ,perl) + ("hmmer" ,hmmer))) + (home-page "https://github.com/tseemann/barrnap") + (synopsis "Ribosomal RNA predictor") + (description + "Barrnap predicts the location of ribosomal RNA genes in genomes. It +supports bacteria (5S, 23S, 16S), archaea (5S,5.8S,23S,16S), mitochondria (12S, +16S) and eukaryotes (5S, 5.8S, 28S, 18S). It takes FASTA DNA sequence as input, +and write GFF3 as output. It uses the NHMMER tool that comes with HMMER for +HMM searching in RNA:DNA style.") + (license (list license:gpl3 + ;; The Rfam HMMs are under cc0, and the SILVA-derived HMMs are + ;; academic-only. + license:cc0 + (license:non-copyleft + "file:///LICENSE.SILVA" + "See LICENSE.SILVA in the distribution."))))) + (define-public bcftools (package (name "bcftools") -- 2.10.2