From f393a2c146d089341c9efebdfe789804b547f06e Mon Sep 17 00:00:00 2001
From: lingnanyuan <1297162327@qq.com>
Date: Wed, 7 Mar 2018 13:45:45 -0600
Subject: [PATCH] orthofinder: Create new package. (#7364)

---
 .../builtin/packages/orthofinder/package.py   | 53 +++++++++++++++++++
 1 file changed, 53 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/orthofinder/package.py

diff --git a/var/spack/repos/builtin/packages/orthofinder/package.py b/var/spack/repos/builtin/packages/orthofinder/package.py
new file mode 100644
index 0000000000..fa620cf1b3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/orthofinder/package.py
@@ -0,0 +1,53 @@
+##############################################################################
+# 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 *
+
+
+class Orthofinder(Package):
+    """OrthoFinder is a fast, accurate and comprehensive analysis tool for
+    comparative genomics.
+
+    It finds orthologues and orthogroups infers rooted  gene trees for all
+    orthogroups and infers a rooted species tree for the species being
+    analysed. OrthoFinder also provides comprehensive statistics for
+    comparative genomic analyses. OrthoFinder is simple to use and all you
+    need to run it is a set of protein sequence files (one per species)
+    in FASTA format."""
+
+    homepage = "https://github.com/davidemms/OrthoFinder"
+    url      = "https://github.com/davidemms/OrthoFinder/releases/download/2.2.0/OrthoFinder-2.2.0.tar.gz"
+
+    version('2.2.0', '4ff585e1eb148fc694a219296fbdd431')
+
+    depends_on('blast-plus', type='run')
+    depends_on('mcl', type='run')
+    depends_on('fastme', type='run')
+    depends_on('py-dlcpar', type='run')
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix.bin)
+
+        chmod = which('chmod')
+        chmod('+x', join_path(prefix.bin, 'orthofinder'))