From 3e72263d79bfe20271e1f0377c4c0047f33ef1a8 Mon Sep 17 00:00:00 2001 From: Audrey Thoma Date: Tue, 18 Jul 2017 13:49:18 -0500 Subject: New package busco (#4678) * busco: new package * busco: fixing fussy paths * removing paths, probably was a problem with our module setup * fixed dep type --- var/spack/repos/builtin/packages/busco/package.py | 59 +++++++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 var/spack/repos/builtin/packages/busco/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/busco/package.py b/var/spack/repos/builtin/packages/busco/package.py new file mode 100644 index 0000000000..ad0f06ca91 --- /dev/null +++ b/var/spack/repos/builtin/packages/busco/package.py @@ -0,0 +1,59 @@ +############################################################################## +# Copyright (c) 2013-2016, 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/llnl/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 * + + +class Busco(PythonPackage): + """Assesses genome assembly and annotation completeness with Benchmarking + Universal Single-Copy Orthologs""" + + homepage = "http://busco.ezlab.org/" + url = "https://gitlab.com/ezlab/busco" + + version('3.0.1', git='https://gitlab.com/ezlab/busco.git', commit='078252e00399550d7b0e8941cd4d986c8e868a83') + version('2.0.1', git='https://gitlab.com/ezlab/busco.git', commit='89aa1ab2527f03a87a214ca90a504ad236582a11') + + depends_on('python', type=('build', 'run')) + depends_on('blast-plus') + depends_on('hmmer') + depends_on('augustus') + + def build(self, spec, prefix): + if self.spec.satisfies('@2.0.1'): + pass + + def install(self, spec, prefix): + if self.spec.satisfies('@3.0.1'): + with working_dir('scripts'): + mkdirp(prefix.bin) + install('generate_plot.py', prefix.bin) + install('run_BUSCO.py', prefix.bin) + install_tree('config', prefix.config) + args = self.install_args(spec, prefix) + self.setup_py('install', *args) + if self.spec.satisfies('@2.0.1'): + mkdirp(prefix.bin) + install('BUSCO.py', prefix.bin) + install('BUSCO_plot.py', prefix.bin) -- cgit v1.2.3-60-g2f50