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snphylo: new package (#7045)

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* pushing partially done recipe for snphylo

* r-snphylo: try

* phylip: added version 3.697

* snphylo: updated package.py

* snphylo: flake8 error fixed
This commit is contained in:
Yifan Zhu 2018-03-21 16:21:55 -05:00 committed by Adam J. Stewart
parent e8a0637606
commit 55f4bbb111
2 changed files with 58 additions and 1 deletions
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2
var/spack/repos/builtin/packages/phylip/package.py
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@ -30,7 +30,7 @@ class Phylip(Package):
inferring phylogenies (evolutionary trees)."""
homepage = "http://evolution.genetics.washington.edu/phylip/"
url = "http://evolution.gs.washington.edu/phylip/download/phylip-3.696.tar.gz"
url = "http://evolution.gs.washington.edu/phylip/download/phylip-3.697.tar.gz"
version('3.697', '0e83d17fb4d668213603c86bc21d9012')
version('3.696', 'dbe5abc26f6089ead3dba41c2db526ee')

57
var/spack/repos/builtin/packages/snphylo/package.py Normal file
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@ -0,0 +1,57 @@
##############################################################################
# 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 *
import distutils.dir_util
class Snphylo(Package):
"""A pipeline to generate a phylogenetic tree from huge SNP data"""
homepage = "http://chibba.pgml.uga.edu/snphylo/"
url = "http://chibba.pgml.uga.edu/snphylo/snphylo.tar.gz"
version('2016-02-04', '467660814965bc9bed6c020c05c0d3a6')
depends_on('python', type=('build', 'run'))
depends_on('r', type=('build', 'run'))
depends_on('r-phangorn', type=('build', 'run'))
depends_on('r-gdsfmt', type=('build', 'run'))
depends_on('r-snprelate', type=('build', 'run'))
depends_on('r-getopt', type=('build', 'run'))
depends_on('muscle')
depends_on('phylip')
def install(self, spec, prefix):
install_answer = ['y', 'y', 'y', 'y']
install_answer_input = 'spack-config.in'
with open(install_answer_input, 'w') as f:
f.writelines(install_answer)
with open(install_answer_input, 'r') as f:
bash = which('bash')
bash('./setup.sh', input=f)
distutils.dir_util.copy_tree(".", prefix)
def setup_environment(self, spack_env, run_env):
run_env.prepend_path('PATH', self.spec.prefix)