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Fixes for augustus package

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- add missing perl dependency
- only filter Makefile if referred to dependency is in the spec
- rewrite the shebang line of scripts to use spack perl
- remove tabix dependency as tabix and bgzip are part of htslib
This commit is contained in:
Glenn P Johnson 2019-09-12 13:21:21 -05:00 committed by Peter Scheibel
parent 2256890d4e
commit b046ee20f5
1 changed files with 23 additions and 13 deletions
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36
var/spack/repos/builtin/packages/augustus/package.py
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@ -4,6 +4,7 @@
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
import glob
class Augustus(MakefilePackage):
@ -22,6 +23,7 @@ class Augustus(MakefilePackage):
version('3.2.3', 'b8c47ea8d0c45aa7bb9a82626c8ff830',
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')
@ -29,7 +31,6 @@ class Augustus(MakefilePackage):
depends_on('htslib', when='@3.3.1:')
depends_on('bcftools', when='@3.3.1:')
depends_on('samtools', when='@3.3.1:')
depends_on('tabix', when='@3.3.1:')
depends_on('curl', when='@3.3.1:')
def edit(self, spec, prefix):
@ -64,19 +65,19 @@ def edit(self, spec, prefix):
with working_dir(join_path('auxprogs', 'bam2wig')):
makefile = FileFilter('Makefile')
# point tools to spack installations
bcftools = self.spec['bcftools'].prefix.include
samtools = self.spec['samtools'].prefix.include
htslib = self.spec['htslib'].prefix.include
tabix = self.spec['tabix'].prefix.include
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=.*$',
'HTSLIB=%s' % htslib)
makefile.filter('SAMTOOLS=.*$',
'SAMTOOLS=%s' % samtools)
makefile.filter('HTSLIB=.*$',
'HTSLIB=%s' % htslib)
makefile.filter('BCFTOOLS=.*$',
'BCFTOOLS=%s' % bcftools)
makefile.filter('TABIX=.*$',
'TABIX=%s' % tabix)
# fix bad linking dirs
makefile.filter('$(SAMTOOLS)/libbam.a',
'$(SAMTOOLS)/../lib/libbam.a', string=True)
@ -88,6 +89,15 @@ def install(self, spec, prefix):
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_environment(self, spack_env, run_env):
run_env.set('AUGUSTUS_CONFIG_PATH', join_path(
self.prefix, 'config'))