braker & genemark-et: new packages (#5058)

* braker & genemark-et: new packages

* fixing install

3 files changed, 106 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/augustus/package.py b/var/spack/repos/builtin/packages/augustus/package.py
index ccaa2f1e70..8a90de639e 100644
--- a/var/spack/repos/builtin/packages/augustus/package.py
+++ b/var/spack/repos/builtin/packages/augustus/package.py
@@ -32,6 +32,7 @@ class Augustus(MakefilePackage):
     homepage = "http://bioinf.uni-greifswald.de/augustus/"
     url      = "http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.2.3.tar.gz"
 
+    version('3.3',   '9ebe494df78ebf6a43091cfc8551050c')
     version('3.2.3', 'b8c47ea8d0c45aa7bb9a82626c8ff830')
 
     depends_on('bamtools')
diff --git a/var/spack/repos/builtin/packages/braker/package.py b/var/spack/repos/builtin/packages/braker/package.py
new file mode 100644
index 0000000000..cfc1f16025
--- /dev/null
+++ b/var/spack/repos/builtin/packages/braker/package.py
@@ -0,0 +1,52 @@
+##############################################################################
+# 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 Braker(Package):
+    """BRAKER is a pipeline for unsupervised RNA-Seq-based genome annotation
+       that combines the advantages of GeneMark-ET and AUGUSTUS"""
+
+    homepage = "http://exon.gatech.edu/braker1.html"
+    url      = "http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER1_v1.11.tar.gz"
+
+    version('1.11', '297efe4cabdd239b710ac2c45d81f6a5')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('augustus')
+    depends_on('genemark-et')
+    depends_on('bamtools')
+    depends_on('samtools')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        mkdirp(prefix.lib)
+        install('braker.pl', prefix.bin)
+        install('filterGenemark.pl', prefix.bin)
+        install('filterIntronsFindStrand.pl', prefix.bin)
+        install('helpMod.pm', prefix.lib)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PERL5LIB', prefix.lib)
diff --git a/var/spack/repos/builtin/packages/genemark-et/package.py b/var/spack/repos/builtin/packages/genemark-et/package.py
new file mode 100644
index 0000000000..352f728290
--- /dev/null
+++ b/var/spack/repos/builtin/packages/genemark-et/package.py
@@ -0,0 +1,53 @@
+##############################################################################
+# 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 *
+import os
+import glob
+
+
+class GenemarkEt(Package):
+    """Gene Prediction in Bacteria, archaea, Metagenomes and
+       Metatranscriptomes."""
+
+    homepage = "http://topaz.gatech.edu/GeneMark"
+
+    version('4.33', '4ab7d7d3277a685dfb49e11bc5b493c3')
+
+    depends_on('perl', type=('build', 'run'))
+
+    def url_for_version(self, version):
+        return "file://{0}/gm_et_linux_64.tar.gz".format(os.getcwd())
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        with working_dir('gmes_petap'):
+            install_tree('lib', prefix.lib)
+            files = glob.iglob('*')
+            for file in files:
+                if os.path.isfile(file):
+                    install(file, prefix.bin)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PERL5LIB', prefix.lib)