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##############################################################################
# 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 glob
import os.path
class Hisat2(MakefilePackage):
"""HISAT2 is a fast and sensitive alignment program for mapping
next-generation sequencing reads (whole-genome, transcriptome, and
exome sequencing data) against the general human population (as well as
against a single reference genome)."""
homepage = "http://ccb.jhu.edu/software/hisat2"
url = "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.1.0-source.zip"
version('2.1.0', '8b566d1b7e6c5801c8ae9824ed2da3d0')
def install(self, spec, prefix):
install_tree('doc', prefix.doc)
install_tree('example', prefix.example)
install_tree('hisatgenotype_modules', prefix.hisatgenotype_modules)
install_tree('hisatgenotype_scripts', prefix.hisatgenotype_scripts)
install_tree('scripts', prefix.scripts)
mkdirp(prefix.bin)
install('hisat2', prefix.bin)
install('hisat2-align-s', prefix.bin)
install('hisat2-align-l', prefix.bin)
install('hisat2-build', prefix.bin)
install('hisat2-build-s', prefix.bin)
install('hisat2-build-l', prefix.bin)
install('hisat2-inspect', prefix.bin)
install('hisat2-inspect-s', prefix.bin)
install('hisat2-inspect-l', prefix.bin)
files = glob.iglob('*.py')
for file in files:
if os.path.isfile(file):
install(file, prefix.bin)
def setup_environment(self, spack_env, run_env):
run_env.prepend_path('PATH', self.spec.prefix)
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