Add Trinity package (#7828)

* Add Trinity package

New package to install Trinity - another odd installer (assumes installation to /usr/local/bin and doesn't copy dot files hence deleting them)

* Update package.py

added dependencies from https://github.com/trinityrnaseq/trinityrnaseq/wiki/Installing-Trinity

* Update package.py

Copy tree to prefix.bin so that PATH can correctly be set for the Trinity command - can't split it off as it seems everything needs to stay together.

* Update package.py

Fixed over-length lines and space before comma

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

@@ -0,0 +1,74 @@
+##############################################################################
+# Copyright (c) 2013-2017, 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/spack/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 *
+from distutils.dir_util import copy_tree
+
+
+class Trinity(MakefilePackage):
+    """Trinity, developed at the Broad Institute and the Hebrew University of
+       Jerusalem, represents a novel method for the efficient and robust de
+       novo reconstruction of transcriptomes from RNA-seq data. Trinity
+       combines three independent software modules: Inchworm, Chrysalis, and
+       Butterfly, applied sequentially to process large volumes of RNA-seq
+       reads. Trinity partitions the sequence data into many individual de
+       Bruijn graphs, each representing the transcriptional complexity at a
+       given gene or locus, and then processes each graph independently to
+       extract full-length splicing isoforms and to tease apart transcripts
+       derived from paralogous genes.
+    """
+
+    homepage = "http://trinityrnaseq.github.io/"
+    url      = "https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.6.6.tar.gz"
+
+    version('2.6.6', 'b7472e98ab36655a6d9296d965471a56')
+
+    depends_on("jdk@8")
+    depends_on("bowtie2")
+    depends_on("jellyfish")
+    depends_on("salmon")
+
+    def build(self, spec, prefix):
+        make
+        make("plugins")
+
+    def install(self, spec, prefix):
+        copy_tree('.', prefix.bin, preserve_symlinks=1)
+        force_remove(join_path(prefix.bin, '.gitmodules'))
+        force_remove(join_path(prefix.bin, 'Butterfly', '.err'))
+        force_remove(join_path(prefix.bin, 'Butterfly', 'src', '.classpath'))
+        force_remove(join_path(prefix.bin, 'Butterfly', 'src', '.err'))
+        force_remove(join_path(prefix.bin, 'Butterfly', 'src', '.project'))
+        remove_linked_tree(join_path(prefix.bin, 'Butterfly', 'src',
+                                     '.settings'))
+        remove_linked_tree(join_path(prefix.bin, 'Inchworm', 'src', '.deps'))
+        remove_linked_tree(join_path(prefix.bin, 'trinity-plugins',
+                                     'ParaFly-0.1.0', 'src', '.deps'))
+        force_remove(join_path(prefix.bin, 'trinity-plugins',
+                               'seqtk-trinity-0.0.2', '.gitignore'))
+        force_remove(join_path(prefix.bin, 'trinity-plugins', 'slclust', 'bin',
+                               '.hidden'))
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('TRINITY_HOME', self.prefix.bin)