53 lines
2.2 KiB
Python
53 lines
2.2 KiB
Python
##############################################################################
|
|
# Copyright (c) 2013-2018, 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 os
|
|
|
|
|
|
class Gapfiller(Package):
|
|
"""GapFiller is a stand-alone program for closing gaps within
|
|
pre-assembled scaffolds.
|
|
|
|
Note: A manual download is required for GapFiller.
|
|
Spack will search your current directory for the download file.
|
|
Alternatively, add this file to a mirror so that Spack can find it.
|
|
For instructions on how to set up a mirror, see
|
|
http://spack.readthedocs.io/en/latest/mirrors.html"""
|
|
|
|
homepage = "https://www.baseclear.com/genomics/bioinformatics/basetools/gapfiller"
|
|
|
|
version('1.10', '54d5e2ada131a1305a66e41c0d380382')
|
|
|
|
def url_for_version(self, version):
|
|
return "file://{0}/39GapFiller_v{1}_linux-x86_64.tar.gz".format(
|
|
os.getcwd(), version.dashed)
|
|
|
|
depends_on('perl', type=('build', 'run'))
|
|
|
|
def install(self, spec, prefix):
|
|
install_tree('bowtie', prefix.bowtie)
|
|
install_tree('bwa', prefix.bwa)
|
|
install('GapFiller.pl', prefix)
|