From 55f4bbb1116cadb7ee5c05d9932d4365b8f919c4 Mon Sep 17 00:00:00 2001 From: Yifan Zhu Date: Wed, 21 Mar 2018 16:21:55 -0500 Subject: [PATCH] snphylo: new package (#7045) * pushing partially done recipe for snphylo * r-snphylo: try * phylip: added version 3.697 * snphylo: updated package.py * snphylo: flake8 error fixed --- .../repos/builtin/packages/phylip/package.py | 2 +- .../repos/builtin/packages/snphylo/package.py | 57 +++++++++++++++++++ 2 files changed, 58 insertions(+), 1 deletion(-) create mode 100644 var/spack/repos/builtin/packages/snphylo/package.py diff --git a/var/spack/repos/builtin/packages/phylip/package.py b/var/spack/repos/builtin/packages/phylip/package.py index d0f82242ca..a26484ce87 100644 --- a/var/spack/repos/builtin/packages/phylip/package.py +++ b/var/spack/repos/builtin/packages/phylip/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/snphylo/package.py b/var/spack/repos/builtin/packages/snphylo/package.py new file mode 100644 index 0000000000..6634835ab1 --- /dev/null +++ b/var/spack/repos/builtin/packages/snphylo/package.py @@ -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)