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-rw-r--r--var/spack/repos/builtin/packages/phyluce/package.py44
1 files changed, 44 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/phyluce/package.py b/var/spack/repos/builtin/packages/phyluce/package.py
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+++ b/var/spack/repos/builtin/packages/phyluce/package.py
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+# 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 *
+
+
+class Phyluce(PythonPackage):
+ """phyluce (phy-loo-chee) is a software package that was initially
+ developed for analyzing data collected from ultraconserved
+ elements in organismal genomes"""
+
+ homepage = "https://github.com/faircloth-lab/phyluce"
+ url = "https://github.com/faircloth-lab/phyluce/archive/v1.6.7.tar.gz"
+
+ version('1.6.7', sha256='98c213ab1610506722ad1440ffc93f9cbc78d8b3aaf3d9a47837e1231452cdb6')
+
+ extends('python')
+ depends_on('python@2.7:', type=('build', 'run'))
+ depends_on('py-setuptools', type=('build', 'run'))
+ depends_on('py-biopython', type='run')
+
+ # runtime binary dependencies
+ depends_on('abyss', type='run')
+ depends_on('bcftools', type='run')
+ depends_on('bwa', type='run')
+ depends_on('gatk', type='run')
+ depends_on('gblocks', type='run')
+ depends_on('lastz', type='run')
+ depends_on('mafft', type='run')
+ depends_on('muscle', type='run')
+ depends_on('picard', type='run')
+ depends_on('raxml+pthreads+sse', type='run')
+ depends_on('samtools', type='run')
+ depends_on('seqtk', type='run')
+ depends_on('spades', type='run')
+ depends_on('trimal', type='run')
+ depends_on('trinity', type='run')
+ depends_on('velvet', type='run')
+
+ def install(self, spec, prefix):
+ python = which('python')
+ python('setup.py', 'install', '--prefix={0}'.format(prefix))