new package: trinotate (starting at 3.1.1) (#9471)

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

@@ -0,0 +1,42 @@
+# Copyright 2013-2018 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 Trinotate(Package):
+    """Trinotate is a comprehensive annotation suite designed for
+       automatic functional annotation of transcriptomes, particularly
+       de novo assembled transcriptomes, from model or non-model organisms"""
+
+    homepage = "https://trinotate.github.io/"
+    url      = "https://github.com/Trinotate/Trinotate/archive/Trinotate-v3.1.1.tar.gz"
+
+    version('3.1.1', sha256='f8af0fa5dbeaaf5a085132cd4ac4f4206b05cc4630f0a17a672c586691f03843')
+
+    depends_on('trinity', type='run')
+    depends_on('transdecoder', type='run')
+    depends_on('sqlite', type='run')
+    depends_on('ncbi-rmblastn', type='run')
+    depends_on('hmmer', type='run')
+    depends_on('perl', type='run')
+    depends_on('lighttpd', type='run')
+    depends_on('perl-dbi', type='run')
+    depends_on('perl-dbd-mysql', type='run')
+    depends_on('perl-cgi', type='run')
+
+    def install(self, spec, prefix):
+        # most of the perl modules have local deps, install the whole tree
+        mkdirp(prefix.lib)
+        install_tree('.', join_path(prefix.lib, 'trinotate'))
+
+        mkdirp(prefix.bin)
+        os.symlink(join_path(prefix.lib, 'trinotate/Trinotate'),
+                   join_path(prefix.bin, 'Trinotate'))
+
+        os.symlink(join_path(prefix.lib,
+                             'trinotate/run_TrinotateWebserver.pl'),
+                   join_path(prefix.bin, 'run_TrinotateWebserver.pl'))