From 11e064d7d1b5b67f876240e4bc1433a3a6640540 Mon Sep 17 00:00:00 2001 From: Eric Date: Thu, 15 Feb 2018 18:23:59 -0600 Subject: new package: pilon (#7033) --- var/spack/repos/builtin/packages/pilon/package.py | 60 +++++++++++++++++++++++ var/spack/repos/builtin/packages/pilon/pilon.sh | 3 ++ 2 files changed, 63 insertions(+) create mode 100644 var/spack/repos/builtin/packages/pilon/package.py create mode 100644 var/spack/repos/builtin/packages/pilon/pilon.sh diff --git a/var/spack/repos/builtin/packages/pilon/package.py b/var/spack/repos/builtin/packages/pilon/package.py new file mode 100644 index 0000000000..a075ce9fd8 --- /dev/null +++ b/var/spack/repos/builtin/packages/pilon/package.py @@ -0,0 +1,60 @@ +############################################################################## +# Copyright (c) 2013-2017, 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/spack/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 * +from shutil import copyfile +import os.path + + +class Pilon(Package): + """Pilon is an automated genome assembly improvement and variant + detection tool.""" + + homepage = "https://github.com/broadinstitute/pilon" + url = "https://github.com/broadinstitute/pilon/releases/download/v1.22/pilon-1.22.jar" + + version('1.22', '3c45568dc1b878a9a0316410ec62ab04', expand=False) + version('1.13', '9e96b4cf4ea595b1996c7e9ca76498b5', expand=False) + + depends_on('java@1.7:', type='run') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + jar_file = 'pilon-{0}.jar'.format(self.version.dotted) + install(jar_file, prefix.bin) + + # Set up a helper script to call java on the jar file, + # explicitly codes the path for java and the jar file. + script_sh = join_path(os.path.dirname(__file__), "pilon.sh") + script = join_path(prefix.bin, "pilon") + copyfile(script_sh, script) + set_executable(script) + + # Munge the helper script to explicitly point to java and the + # jar file. + java = join_path(self.spec['java'].prefix, 'bin', 'java') + kwargs = {'ignore_absent': False, 'backup': False, 'string': False} + filter_file('^java', java, script, **kwargs) + filter_file('pilon-{0}.jar', join_path(prefix.bin, jar_file), + script, **kwargs) diff --git a/var/spack/repos/builtin/packages/pilon/pilon.sh b/var/spack/repos/builtin/packages/pilon/pilon.sh new file mode 100644 index 0000000000..41a31b3407 --- /dev/null +++ b/var/spack/repos/builtin/packages/pilon/pilon.sh @@ -0,0 +1,3 @@ +#!/bin/sh +# convenience wrapper for the pilon jar file +java -jar pilon.jar "$@" -- cgit v1.2.3-70-g09d2