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Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/phyluce/package.py | 44 |
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 new file mode 100644 index 0000000000..3a28108ace --- /dev/null +++ b/var/spack/repos/builtin/packages/phyluce/package.py @@ -0,0 +1,44 @@ +# 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)) |