figtree: new package starting at 1.4.3 (#9359)

* figtree: new package starting at 1.4.3

* figtree: add java dep

* figtree: use portable octal format

* figtree: remove boilerplate

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

@@ -0,0 +1,58 @@
+##############################################################################
+# Copyright (c) 2013-2018, 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/spack/spack
+# Please also see the NOTICE and LICENSE files 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 *
+import os
+
+
+class Figtree(Package):
+    """FigTree is designed as a graphical viewer of phylogenetic trees and
+       as a program for producing publication-ready figures. As with most of
+       my programs, it was written for my own needs so may not be as polished
+       and feature-complete as a commercial program. In particular it is
+       designed to display summarized and annotated trees produced by BEAST."""
+
+    homepage = "https://github.com/rambaut/figtree"
+    url      = "https://github.com/rambaut/figtree/releases/download/v1.4.3/FigTree_v1.4.3.tgz"
+
+    version('1.4.3', sha256='f497d4dd3a6d220f6b62495b6f47a12ade50d87dbd8d6089f168e94d202f937b')
+
+    depends_on('java', type='run')
+
+    def patch(self):
+        # we have to change up the executable to point to the right program
+        filter_file('lib/figtree.jar',
+                    join_path(self.spec.prefix.lib, 'figtree.jar'),
+                    'bin/figtree', string=True)
+
+        # also set proper executable flags
+        os.chmod('bin/figtree', 0o775)
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install_tree('bin', prefix.bin)
+
+        mkdirp(prefix.lib)
+        install_tree('lib', prefix.lib)