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# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
import glob
class Augustus(MakefilePackage):
"""AUGUSTUS is a program that predicts genes in eukaryotic
genomic sequences"""
homepage = "http://bioinf.uni-greifswald.de/augustus/"
url = "https://github.com/Gaius-Augustus/Augustus/archive/3.3.2.tar.gz"
# Releases have moved to github
version('3.3.2', sha256='d09f972cfd88deb34b19b69878eb8af3bbbe4f1cde1434b69cedc2aa6247a0f2')
version('3.3.1-tag1', sha256='011379606f381ee21b9716f83e8a1a57b2aaa01aefeebd2748104efa08c47cab',
url='https://github.com/Gaius-Augustus/Augustus/archive/v3.3.1-tag1.tar.gz')
version('3.3', sha256='b5eb811a4c33a2cc3bbd16355e19d530eeac6d1ac923e59f48d7a79f396234ee',
url='http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.3.tar.gz')
version('3.2.3', sha256='a1af128aefd228dea0c46d6f5234910fdf068a2b9133175ca8da3af639cb4514',
url='http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.2.3.tar.gz')
depends_on('perl', type=('build', 'run'))
depends_on('bamtools')
depends_on('gsl')
depends_on('boost')
depends_on('zlib')
depends_on('htslib', when='@3.3.1:')
depends_on('bcftools', when='@3.3.1:')
depends_on('samtools', when='@3.3.1:')
depends_on('curl', when='@3.3.1:')
def edit(self, spec, prefix):
# Set compile commands for each compiler and
# Fix for using 'boost' on Spack. (only after ver.3.3.1-tag1)
if self.version >= Version('3.3.1-tag1'):
with working_dir(join_path('auxprogs', 'utrrnaseq', 'Debug')):
filter_file('g++', spack_cxx, 'makefile', string=True)
filter_file('g++ -I/usr/include/boost', '{0} -I{1}'
.format(spack_cxx,
self.spec['boost'].prefix.include),
'src/subdir.mk', string=True)
# Set compile commands to all makefiles.
makefiles = [
'auxprogs/aln2wig/Makefile',
'auxprogs/bam2hints/Makefile',
'auxprogs/bam2wig/Makefile',
'auxprogs/checkTargetSortedness/Makefile',
'auxprogs/compileSpliceCands/Makefile',
'auxprogs/homGeneMapping/src/Makefile',
'auxprogs/joingenes/Makefile',
'src/Makefile'
]
for makefile in makefiles:
filter_file('gcc', spack_cc, makefile, string=True)
filter_file('g++', spack_cxx, makefile, string=True)
with working_dir(join_path('auxprogs', 'filterBam', 'src')):
makefile = FileFilter('Makefile')
makefile.filter('BAMTOOLS = .*', 'BAMTOOLS = %s' % self.spec[
'bamtools'].prefix)
makefile.filter('INCLUDES = *',
'INCLUDES = -I$(BAMTOOLS)/include/bamtools ')
if 'bamtools@2.5:' in spec:
makefile.filter('LIBS = -lbamtools -lz',
'LIBS = $(BAMTOOLS)/lib64/'
'/libbamtools.a -lz')
if 'bamtools@:2.4' in spec:
makefile.filter('LIBS = -lbamtools -lz',
'LIBS = $(BAMTOOLS)/lib/bamtools'
'/libbamtools.a -lz')
with working_dir(join_path('auxprogs', 'bam2hints')):
makefile = FileFilter('Makefile')
makefile.filter('# Variable definition',
'BAMTOOLS = %s' % self.spec['bamtools'].prefix)
makefile.filter('INCLUDES = /usr/include/bamtools',
'INCLUDES = $(BAMTOOLS)/include/bamtools')
if 'bamtools@2.5:' in spec:
makefile.filter('LIBS = -lbamtools -lz',
'LIBS = $(BAMTOOLS)/lib64/'
'/libbamtools.a -lz')
if 'bamtools@:2.4' in spec:
makefile.filter('LIBS = -lbamtools -lz',
'LIBS = $(BAMTOOLS)/lib/bamtools'
'/libbamtools.a -lz')
with working_dir(join_path('auxprogs', 'bam2wig')):
makefile = FileFilter('Makefile')
# point tools to spack installations
if 'bcftools' in spec:
bcftools = self.spec['bcftools'].prefix.include
makefile.filter('BCFTOOLS=.*$',
'BCFTOOLS=%s' % bcftools)
if 'samtools' in spec:
samtools = self.spec['samtools'].prefix.include
makefile.filter('SAMTOOLS=.*$',
'SAMTOOLS=%s' % samtools)
if 'htslib' in spec:
htslib = self.spec['htslib'].prefix.include
makefile.filter('HTSLIB=.*$',
'HTSLIB=%s' % htslib)
# fix bad linking dirs
makefile.filter('$(SAMTOOLS)/libbam.a',
'$(SAMTOOLS)/../lib/libbam.a', string=True)
makefile.filter('$(HTSLIB)/libhts.a',
'$(HTSLIB)/../lib/libhts.a', string=True)
def install(self, spec, prefix):
install_tree('bin', join_path(self.spec.prefix, 'bin'))
install_tree('config', join_path(self.spec.prefix, 'config'))
install_tree('scripts', join_path(self.spec.prefix, 'scripts'))
@run_after('install')
def filter_sbang(self):
with working_dir(self.prefix.scripts):
pattern = '^#!.*/usr/bin/perl'
repl = '#!{0}'.format(self.spec['perl'].command.path)
files = glob.iglob("*.pl")
for file in files:
filter_file(pattern, repl, *files, backup=False)
def setup_run_environment(self, env):
env.set('AUGUSTUS_CONFIG_PATH', join_path(
self.prefix, 'config'))
env.prepend_path('PATH', join_path(self.prefix, 'scripts'))
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