New package busco (#4678)

* busco: new package

* busco: fixing fussy paths

* removing paths, probably was a problem with our module setup

* fixed dep type

1 files changed, 59 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/busco/package.py b/var/spack/repos/builtin/packages/busco/package.py
new file mode 100644
index 0000000000..ad0f06ca91
--- /dev/null
+++ b/var/spack/repos/builtin/packages/busco/package.py
@@ -0,0 +1,59 @@
+##############################################################################
+# 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 Busco(PythonPackage):
+    """Assesses genome assembly and annotation completeness with Benchmarking
+       Universal Single-Copy Orthologs"""
+
+    homepage = "http://busco.ezlab.org/"
+    url      = "https://gitlab.com/ezlab/busco"
+
+    version('3.0.1', git='https://gitlab.com/ezlab/busco.git', commit='078252e00399550d7b0e8941cd4d986c8e868a83')
+    version('2.0.1', git='https://gitlab.com/ezlab/busco.git', commit='89aa1ab2527f03a87a214ca90a504ad236582a11')
+
+    depends_on('python', type=('build', 'run'))
+    depends_on('blast-plus')
+    depends_on('hmmer')
+    depends_on('augustus')
+
+    def build(self, spec, prefix):
+        if self.spec.satisfies('@2.0.1'):
+            pass
+
+    def install(self, spec, prefix):
+        if self.spec.satisfies('@3.0.1'):
+            with working_dir('scripts'):
+                mkdirp(prefix.bin)
+                install('generate_plot.py', prefix.bin)
+                install('run_BUSCO.py', prefix.bin)
+            install_tree('config', prefix.config)
+            args = self.install_args(spec, prefix)
+            self.setup_py('install', *args)
+        if self.spec.satisfies('@2.0.1'):
+            mkdirp(prefix.bin)
+            install('BUSCO.py', prefix.bin)
+            install('BUSCO_plot.py', prefix.bin)