From 668233a81936e60a4327d4275cf978d831e364a8 Mon Sep 17 00:00:00 2001 From: Audrey Thoma Date: Tue, 25 Jul 2017 15:50:23 -0500 Subject: trimgalore: new package (#4899) --- .../repos/builtin/packages/trimgalore/package.py | 44 ++++++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 var/spack/repos/builtin/packages/trimgalore/package.py diff --git a/var/spack/repos/builtin/packages/trimgalore/package.py b/var/spack/repos/builtin/packages/trimgalore/package.py new file mode 100644 index 0000000000..9dd8be11e9 --- /dev/null +++ b/var/spack/repos/builtin/packages/trimgalore/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Trimgalore(Package): + """Trim Galore! is a wrapper around Cutadapt and FastQC to consistently + apply adapter and quality trimming to FastQ files, with extra + functionality for RRBS data.""" + + homepage = "https://github.com/FelixKrueger/TrimGalore" + url = "https://github.com/FelixKrueger/TrimGalore/archive/0.4.4.tar.gz" + + version('0.4.4', 'aae1b807b48e38bae7074470203997bb') + + depends_on('perl', type=('build', 'run')) + depends_on('py-cutadapt', type=('build', 'run')) + depends_on('fastqc') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install('trim_galore', prefix.bin) -- cgit v1.2.3-70-g09d2