treesub: new package starting at 0.2 (#9361)

* treesub: new package starting at 0.2

* treesub: fix ant build, add exec script

* treesub: use portable octal format

* treesub: add license header

not sure how it even went missing.

2 files changed, 63 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/treesub/package.py b/var/spack/repos/builtin/packages/treesub/package.py
new file mode 100644
index 0000000000..6cec60fa22
--- /dev/null
+++ b/var/spack/repos/builtin/packages/treesub/package.py
@@ -0,0 +1,61 @@
+##############################################################################
+# 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 Treesub(Package):
+    """A small program (which glues together other programs) that
+       allows a user to input a codon alignment in FASTA format and
+       produce an annotated phylogenetic tree showing which substitutions
+       occurred on a given branch. Originally written for colleagues at
+       the MRC NIMR."""
+
+    homepage = "https:/github.com/tamuri/treesub"
+    url      = "https://github.com/tamuri/treesub/archive/v0.2.tar.gz"
+
+    version('0.2', sha256='58b0d2638cf9ae1ad8705df26a57c32b52a69f50e7954debbd678c82772fdc56')
+    version('0.1', sha256='c083ecc5f7e9f11645a7e768f6a09fefcbb254b526212003527b4b8dd14723f1')
+
+    depends_on('jdk', type='run')
+    depends_on('ant', type='build')
+    depends_on('paml', type='run')
+    depends_on('raxml', type='run')
+    depends_on('figtree', type='run')
+
+    def install(self, spec, prefix):
+        ant = self.spec['ant'].command
+        ant('jar')
+
+        mkdirp(prefix.bin)
+        install_tree('dist', prefix.bin)
+
+        mkdirp(prefix.lib)
+        install_tree('lib', prefix.lib)
+
+        execscript = join_path(self.package_dir, 'treesub')
+        os.chmod(execscript, 0o775)
+        install(execscript, prefix.bin)
diff --git a/var/spack/repos/builtin/packages/treesub/treesub b/var/spack/repos/builtin/packages/treesub/treesub
new file mode 100755
index 0000000000..8be7cb73e6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/treesub/treesub
@@ -0,0 +1,2 @@
+#!/bin/sh
+java -jar $(dirname $0)/treesub.jar