guidance: new package (#6079)

* guidance: new package

* not really fixed yet

* adding loop

* fixing url

* dang typos

1 files changed, 66 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/guidance/package.py b/var/spack/repos/builtin/packages/guidance/package.py
new file mode 100644
index 0000000000..6cb4e0cfc6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/guidance/package.py
@@ -0,0 +1,66 @@
+##############################################################################
+# 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/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 glob
+
+
+class Guidance(MakefilePackage):
+    """Guidance: Accurate detection of unreliable alignment regions accounting
+       for the uncertainty of multiple parameters."""
+
+    homepage = "http://guidance.tau.ac.il/ver2/"
+    url      = "http://guidance.tau.ac.il/ver2/guidance.v2.02.tar.gz"
+
+    version('2.02', 'aa6ae2168e8e0237ee56bc2ac81202cf')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('perl-bio-perl', type=('build', 'run'))
+    depends_on('ruby')
+    depends_on('prank')
+    depends_on('clustalw')
+    depends_on('mafft')
+    depends_on('muscle')
+
+    conflicts('%gcc@6.2.0:')
+
+    def edit(self, spec, prefix):
+        for dir in 'Guidance', 'Selecton', 'bioSequence_scripts_and_constants':
+            with working_dir(join_path('www', dir)):
+                files = glob.iglob('*.pl')
+                for file in files:
+                    perl = FileFilter(file)
+                    perl.filter('#!/usr/bin/perl -w', '#!/usr/bin/env perl')
+
+    def install(self, spac, prefix):
+        mkdir(prefix.bin)
+        install_tree('libs', prefix.bin.libs)
+        install_tree('programs', prefix.bin.programs)
+        install_tree('www', prefix.bin.www)
+        with working_dir(join_path('www', 'Guidance')):  # copy without suffix
+            install('guidance.pl', join_path(prefix.bin.www.Guidance,
+                                             'guidance'))
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', prefix.bin.www.Guidance)