1 files changed, 62 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/gatk/package.py b/var/spack/repos/builtin/packages/gatk/package.py
new file mode 100644
index 0000000000..32bb771530
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gatk/package.py
@@ -0,0 +1,62 @@
+# 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 glob
+import os.path
+import re
+
+
+class Gatk(Package):
+    """Genome Analysis Toolkit
+       Variant Discovery in High-Throughput Sequencing Data
+    """
+    homepage = "https://software.broadinstitute.org/gatk/"
+    url      = "https://github.com/broadinstitute/gatk/releases/download/4.0.4.0/gatk-4.0.4.0.zip"
+
+    version('4.0.8.1', sha256='6d47463dfd8c16ffae82fd29e4e73503e5b7cd0fcc6fea2ed50ee3760dd9acd9',
+            url='https://github.com/broadinstitute/gatk/archive/4.0.8.1.tar.gz')
+    version('4.0.4.0', '083d655883fb251e837eb2458141fc2b',
+            url="https://github.com/broadinstitute/gatk/releases/download/4.0.4.0/gatk-4.0.4.0.zip")
+    version('3.8-0', '0581308d2a25f10d11d3dfd0d6e4d28e', extension='tar.gz',
+            url="https://software.broadinstitute.org/gatk/download/auth?package=GATK")
+
+    depends_on('java@8:', type='run')
+    depends_on('python@2.6:2.8,3.6:', type='run', when='@4.0:')
+    depends_on('r@3.2:', type='run', when='@4.0:')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+
+        # Install all executable non-script files to prefix bin
+        files = [x for x in glob.glob("*")
+                 if not re.match("^.*\.sh$", x) and is_exe(x)]
+        for f in files:
+            install(f, prefix.bin)
+
+        # Skip helper script settings
+        if spec.satisfies('@:4.0'):
+            return
+
+        # 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__), "gatk.sh")
+        script = join_path(prefix.bin, "gatk")
+        install(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('GenomeAnalysisTK.jar', join_path(prefix.bin,
+                    'GenomeAnalysisTK.jar'),
+                    script, **kwargs)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('GATK',
+                             join_path(self.prefix, 'bin',
+                                                    'GenomeAnalysisTK.jar'))