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Diffstat (limited to 'var/spack/repos/builtin/packages/igvtools/package.py')
-rw-r--r-- | var/spack/repos/builtin/packages/igvtools/package.py | 40 |
1 files changed, 40 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/igvtools/package.py b/var/spack/repos/builtin/packages/igvtools/package.py new file mode 100644 index 0000000000..8e57a57fb3 --- /dev/null +++ b/var/spack/repos/builtin/packages/igvtools/package.py @@ -0,0 +1,40 @@ +# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * +import os + + +class Igvtools(Package): + """IGVTools suite of command-line utilities for preprocessing data + files""" + + homepage = "https://software.broadinstitute.org/software/igv/home" + url = "http://data.broadinstitute.org/igv/projects/downloads/2.3/igvtools_2.3.98.zip" + + version('2.3.98', '17ed12a213cd9cdaeb2f2a5c56d84bc4') + + depends_on('java@8:') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + jar_file = 'igvtools.jar' + install(jar_file, prefix.bin) + install_tree('genomes', prefix.genomes) + + # 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__), "igvtools.sh") + script = prefix.bin.igvtools + install(script_sh, script) + set_executable(script) + + # Munge the helper script to explicitly point to java and the + # jar file. + java = spec['jdk'].prefix.bin.java + kwargs = {'ignore_absent': False, 'backup': False, 'string': False} + filter_file('^java', java, script, **kwargs) + filter_file(jar_file, join_path(prefix.bin, jar_file), + script, **kwargs) |