From cf796ed595c0fc05e0648fc983138ea1af93489a Mon Sep 17 00:00:00 2001 From: Audrey Thoma Date: Thu, 17 Aug 2017 15:32:30 -0500 Subject: pagit: new package (#5140) * pagit: new package * removed unneeded env var --- var/spack/repos/builtin/packages/pagit/package.py | 68 +++++++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 var/spack/repos/builtin/packages/pagit/package.py diff --git a/var/spack/repos/builtin/packages/pagit/package.py b/var/spack/repos/builtin/packages/pagit/package.py new file mode 100644 index 0000000000..2e41d83da3 --- /dev/null +++ b/var/spack/repos/builtin/packages/pagit/package.py @@ -0,0 +1,68 @@ +############################################################################## +# 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 Pagit(Package): + """PAGIT addresses the need for software to generate high quality draft + genomes.""" + + homepage = "http://www.sanger.ac.uk/science/tools/pagit" + url = "ftp://ftp.sanger.ac.uk/pub/resources/software/pagit/PAGIT.V1.01.64bit.tgz" + + version('1.01', '2c4e8512c8c02073146b50b328962e9d') + + depends_on('java', type=('build', 'run')) + depends_on('perl', type=('build', 'run')) + + def url_for_version(self, version): + url = 'ftp://ftp.sanger.ac.uk/pub/resources/software/pagit/PAGIT.V{0}.64bit.tgz' + return url.format(version) + + def install(self, spec, prefix): + with working_dir('PAGIT'): + install_tree('ABACAS', prefix.ABACAS) + install_tree('bin', prefix.bin) + install_tree('ICORN', prefix.ICORN) + install_tree('IMAGE', prefix.IMAGE) + install_tree('lib', prefix.lib) + install_tree('RATT', prefix.RATT) + + def setup_environment(self, spack_env, run_env): + run_env.set('PAGIT_HOME', self.prefix) + run_env.set('PILEUP_HOME', join_path(self.prefix.bin, 'pileup_v0.5')) + run_env.set('ICORN_HOME', self.prefix.icorn) + run_env.set('SNPOMATIC_HOME', self.prefix.bin) + run_env.set('RATT_HOME', self.prefix.RATT) + run_env.set('RATT_CONFIG', join_path(self.prefix.RATT, 'RATT_config')) + run_env.prepend_path('PATH', join_path(self.prefix.bin, 'pileup_v0.5', + 'ssaha2')) + run_env.prepend_path('PATH', join_path(self.prefix.bin, + 'pileup_v0.5')) + run_env.prepend_path('PATH', self.prefix.IMAGE) + run_env.prepend_path('PATH', self.prefix.ABACAS) + run_env.prepend_path('PATH', self.prefix.ICORN) + run_env.prepend_path('PATH', self.prefix.RATT) + run_env.prepend_path('PERL5LIB', self.prefix.lib) -- cgit v1.2.3-70-g09d2