From b62f0962b0f4bf0d31c303789ead30e17a7aa72a Mon Sep 17 00:00:00 2001 From: Audrey Thoma Date: Wed, 26 Jul 2017 10:14:55 -0500 Subject: shortstack: new package (#4905) --- .../repos/builtin/packages/shortstack/package.py | 45 ++++++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 var/spack/repos/builtin/packages/shortstack/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/shortstack/package.py b/var/spack/repos/builtin/packages/shortstack/package.py new file mode 100644 index 0000000000..8feb671013 --- /dev/null +++ b/var/spack/repos/builtin/packages/shortstack/package.py @@ -0,0 +1,45 @@ +############################################################################## +# 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 Shortstack(Package): + """ShortStack is a tool developed to process and analyze smallRNA-seq data + with respect to a reference genome, and output a comprehensive and + informative annotation of all discovered small RNA genes.""" + + homepage = "http://sites.psu.edu/axtell/software/shortstack/" + url = "https://github.com/MikeAxtell/ShortStack/archive/v3.8.3.tar.gz" + + version('3.8.3', '3f21f494f799039f3fa88ea343f2d20d') + + depends_on('perl', type=('build', 'run')) + depends_on('samtools') + depends_on('viennarna') + depends_on('bowtie') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install('ShortStack', prefix.bin) -- cgit v1.2.3-60-g2f50