orthofiller: new package at 1.1.4 (#10373)

var/spack/repos/builtin/packages/orthofiller/package.py

@@ -0,0 +1,38 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Orthofiller(Package):
+    """OrthoFiller: Identifying missing annotations for evolutionarily
+       conserved genes."""
+
+    homepage = "https://github.com/mpdunne/orthofiller/"
+    url      = "https://github.com/mpdunne/orthofiller/archive/1.1.4.tar.gz"
+
+    version('1.1.4', sha256='a693a3372a3f05041ce30cbf84da1be88e85eae4effe32dbd7809ccef119a295')
+
+    depends_on('augustus', type='run')
+    depends_on('bedtools2@2.25.0', type='run')
+    depends_on('hmmer', type='run')
+    depends_on('orthofinder', type='run')
+    depends_on('python@2.7:', type='run')
+    depends_on('py-biopython', type='run')
+    depends_on('py-scipy', type='run')
+    depends_on('r', type='run')
+    depends_on('r-gamlss', type='run')
+    depends_on('mafft', type='run')
+
+    def install(self, spec, prefix):
+        # orthofiller tests for common unix programs using man
+        # runtime modules will quickly overflow the maximum MANPATH;
+        # we change the man tests to use which instead, more reliable anyway
+        filter_file('"man "', '"which "', 'OrthoFiller.py', string=True)
+
+        os.chmod('OrthoFiller.py', 0o755)
+        mkdirp(prefix.bin)
+        install('OrthoFiller.py', prefix.bin)