diff options
4 files changed, 86 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/cromwell-womtool/package.py b/var/spack/repos/builtin/packages/cromwell-womtool/package.py new file mode 100644 index 0000000000..4256e8ffc8 --- /dev/null +++ b/var/spack/repos/builtin/packages/cromwell-womtool/package.py @@ -0,0 +1,40 @@ +# Copyright 2013-2019 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.path + + +class CromwellWomtool(Package): + """Command line utilities for interacting with the + Workflow Object Model (WOM). + """ + + homepage = "https://cromwell.readthedocs.io/en/stable/WOMtool/" + url = "https://github.com/broadinstitute/cromwell/releases/download/44/womtool-44.jar" + + version('44', sha256='b17c0f4933d7b136c7d9760f7858f6439e3c6371f12492e2aeaab3209c28f80a', expand=False) + + depends_on('java@8', type='run') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + jar_file = 'womtool-{0}.jar'.format(self.version) + 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__), "womtool.sh") + script = prefix.bin.womtool + install(script_sh, script) + set_executable(script) + + # Munge the helper script to explicitly point to java and the + # jar file. + java = self.spec['java'].prefix.bin.java + kwargs = {'ignore_absent': False, 'backup': False, 'string': False} + filter_file('^java', java, script, **kwargs) + filter_file('womtool.jar', join_path(prefix.bin, jar_file), + script, **kwargs) diff --git a/var/spack/repos/builtin/packages/cromwell-womtool/womtool.sh b/var/spack/repos/builtin/packages/cromwell-womtool/womtool.sh new file mode 100644 index 0000000000..a5f64cb64b --- /dev/null +++ b/var/spack/repos/builtin/packages/cromwell-womtool/womtool.sh @@ -0,0 +1,3 @@ +#!/bin/sh +# convenience wrapper for the picard womtool jar file +java -jar womtool.jar "$@" diff --git a/var/spack/repos/builtin/packages/cromwell/cromwell.sh b/var/spack/repos/builtin/packages/cromwell/cromwell.sh new file mode 100644 index 0000000000..5ed99432f6 --- /dev/null +++ b/var/spack/repos/builtin/packages/cromwell/cromwell.sh @@ -0,0 +1,3 @@ +#!/bin/sh +# convenience wrapper for the cromwell jar file +java -jar cromwell.jar "$@" diff --git a/var/spack/repos/builtin/packages/cromwell/package.py b/var/spack/repos/builtin/packages/cromwell/package.py new file mode 100644 index 0000000000..cb1562cc20 --- /dev/null +++ b/var/spack/repos/builtin/packages/cromwell/package.py @@ -0,0 +1,40 @@ +# Copyright 2013-2019 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.path + + +class Cromwell(Package): + """Cromwell is a Workflow Management System geared towards scientific + workflows. + """ + + homepage = "http://cromwell.readthedocs.io/" + url = "https://github.com/broadinstitute/cromwell/releases/download/44/cromwell-44.jar" + + version('44', sha256='8b411673f6b3c835c6031db3094a7404b9a371133794046fd295719d61e56db0', expand=False) + + depends_on('java@8', type='run') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + jar_file = 'cromwell-{0}.jar'.format(self.version) + 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__), "cromwell.sh") + script = prefix.bin.cromwell + install(script_sh, script) + set_executable(script) + + # Munge the helper script to explicitly point to java and the + # jar file. + java = self.spec['java'].prefix.bin.java + kwargs = {'ignore_absent': False, 'backup': False, 'string': False} + filter_file('^java', java, script, **kwargs) + filter_file('cromwell.jar', join_path(prefix.bin, jar_file), + script, **kwargs) |