new package: Cromwell (#12309)

* add new package cromwell

* fix flake8 errors, add cromwell-womtool package

* change name of cromwell to cromwell-server

* renamed cromwell-server to just cromwell

* update description to what is in the project docs

* fixing format call for python2.6 compatibility

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)