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authorJustin Stanley <molecuul@users.noreply.github.com>2018-10-18 13:47:46 -0500
committerPeter Scheibel <scheibel1@llnl.gov>2018-10-18 11:47:46 -0700
commita2dc958248961cde445bac237ece5e047a25be5f (patch)
treeaa730f3082605882eb0693aa0ea2b55f5294983c /var
parent3228f0af57e0a29c091257590eadce835fcc8d89 (diff)
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new package: trinotate (starting at 3.1.1) (#9471)
Diffstat (limited to 'var')
-rw-r--r--var/spack/repos/builtin/packages/trinotate/package.py42
1 files changed, 42 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/trinotate/package.py b/var/spack/repos/builtin/packages/trinotate/package.py
new file mode 100644
index 0000000000..718a061ba8
--- /dev/null
+++ b/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'))