tppred: new package (#5091)

* tppred: new package

* fixed url_for_version

* fixed version spec on dependency

* removing unneeded dependency

2 files changed, 55 insertions, 1 deletions

diff --git a/var/spack/repos/builtin/packages/py-scikit-learn/package.py b/var/spack/repos/builtin/packages/py-scikit-learn/package.py
index 9817ff815b..0d2a9a155c 100644
--- a/var/spack/repos/builtin/packages/py-scikit-learn/package.py
+++ b/var/spack/repos/builtin/packages/py-scikit-learn/package.py
@@ -35,8 +35,8 @@ class PyScikitLearn(PythonPackage):
     version('0.15.2', 'd9822ad0238e17b382a3c756ea94fe0d')
     version('0.16.1', '363ddda501e3b6b61726aa40b8dbdb7e')
     version('0.17.1', 'a2f8b877e6d99b1ed737144f5a478dfc')
+    version('0.13.1', 'acba398e1d46274b8470f40d0926e6a4')
 
     depends_on('python@2.6:2.8,3.3:')
-    depends_on('py-setuptools',   type='build')
     depends_on('py-numpy@1.6.1:', type=('build', 'run'))
     depends_on('py-scipy@0.9:',   type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/tppred/package.py b/var/spack/repos/builtin/packages/tppred/package.py
new file mode 100644
index 0000000000..919e15c3b0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tppred/package.py
@@ -0,0 +1,54 @@
+##############################################################################
+# 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 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 *
+
+
+class Tppred(Package):
+    """TPPRED is a software package for the prediction of mitochondrial
+       targeting peptides from protein primary sequence."""
+
+    homepage = "https://tppred2.biocomp.unibo.it/tppred2/default/software"
+    url      = "http://biocomp.unibo.it/savojard/tppred2.tar.gz"
+
+    version('2.0', 'cd848569f6a8aa51d18fbe55fe45d624')
+
+    depends_on('python@2.7:2.999', type='run')
+    depends_on('py-scikit-learn@0.13.1', type='run')
+    depends_on('emboss')
+
+    def url_for_version(self, version):
+        url = 'http://biocomp.unibo.it/savojard/tppred{0}.tar.gz'
+        return url.format(version.up_to(1))
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        with working_dir('bin'):
+            install('tppred2.py', prefix.bin)
+        install_tree('data', prefix.data)
+        install_tree('example', prefix.example)
+        install_tree('tppred2modules', prefix.modules)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('TPPRED_ROOT', prefix)