diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/beagle/beagle.sh | 4 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/beagle/package.py | 43 |
2 files changed, 47 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/beagle/beagle.sh b/var/spack/repos/builtin/packages/beagle/beagle.sh new file mode 100644 index 0000000000..58093103f3 --- /dev/null +++ b/var/spack/repos/builtin/packages/beagle/beagle.sh @@ -0,0 +1,4 @@ +#!/bin/sh +# convenience wrapper for the jar file +java $JAVA_ARGS $JAVA_OPTS -jar beagle.jar "$@" + diff --git a/var/spack/repos/builtin/packages/beagle/package.py b/var/spack/repos/builtin/packages/beagle/package.py new file mode 100644 index 0000000000..391807db42 --- /dev/null +++ b/var/spack/repos/builtin/packages/beagle/package.py @@ -0,0 +1,43 @@ +# 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 Beagle(Package): + """Beagle is a software package for phasing genotypes and for imputing + ungenotyped markers.""" + + homepage = "http://faculty.washington.edu/browning/beagle/beagle.html" + + version('5.1', sha256='994f926a4ec0eac665631f37c4a961d3f75c966c71841079275364013c90996c', + expand=False, url='http://faculty.washington.edu/browning/beagle/beagle.25Nov19.28d.jar') + version('5.0', sha256='8390fe18b53786b676b67dddae6d1c086d6225e518f6a82047f4138196b48621', + expand=False, url='https://faculty.washington.edu/browning/beagle/beagle.12Jul19.0df.jar') + version('4.1', sha256='6c94610b278fc108c3e80b1134226911be1fc92b7d378ba648ac3eb97c5a3207', + expand=False, url='https://faculty.washington.edu/browning/beagle/beagle.27Jan18.7e1.jar') + + depends_on('java@8', type='run') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + jar_file = os.path.basename(self.stage.archive_file) + 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__), "beagle.sh") + script = prefix.bin.beagle + 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('beagle.jar', join_path(prefix.bin, jar_file), + script, **kwargs) |