Add a package for Trimmomatic (#4399)

* Add a package for Trimmomatic

See the discussion about installing jar files in #4386.

Also installs a wrapper script that has explicit references to the prerequisite java exe and to the jar file in it's final resting place.

* Fix bad format statement

Apparently something like this "blah{}".format(...) works (it's missing
something inside the curly braces) but fails the travis test.

var/spack/repos/builtin/packages/trimmomatic/package.py

@@ -0,0 +1,65 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+from distutils.dir_util import copy_tree
+from shutil import copyfile
+import os.path
+
+
+class Trimmomatic(Package):
+    """A flexible read trimming tool for Illumina NGS data."""
+
+    homepage = "http://www.usadellab.org/cms/?page=trimmomatic"
+    url      = "http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip"
+
+    # Older version aren't explicitly made available, but the URL
+    # works as we'd like it to, so...
+    version('0.36', '8549130d86b6f0382b1a71a2eb45de39')
+    version('0.33', '924fc8eb38fdff71740a0e05d32d6a2b')
+
+    depends_on('jdk@8:', type='run')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        jar_file = 'trimmomatic-{v}.jar'.format(v=self.version.dotted)
+        install(jar_file, prefix.bin)
+
+        # Put the adapter files someplace sensible
+        copy_tree('adapters', join_path(self.prefix.share, 'adapters'))
+
+        # 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__), "trimmomatic.sh")
+        script = join_path(prefix.bin, "trimmomatic")
+        copyfile(script_sh, script)
+        set_executable(script)
+
+        # Munge the helper script to explicitly point to java and the
+        # jar file.
+        java = join_path(self.spec['jdk'].prefix, 'bin', 'java')
+        kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
+        filter_file('^java', java, script, **kwargs)
+        filter_file('trimmomatic.jar', join_path(prefix.bin, jar_file),
+                    script, **kwargs)

var/spack/repos/builtin/packages/trimmomatic/trimmomatic.sh

@@ -0,0 +1,3 @@
+#!/bin/sh
+# convenience wrapper for the trimmomatic.jar file
+java -jar trimmomatic.jar "$@"