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augustus: fix bam2wig auxprog build (#10362)

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* augustus: fix bam2wig auxprog build

* augustus: few more changes to make new versions work
This commit is contained in:
Justin Stanley 2019-02-04 10:36:10 -06:00 committed by Levi Baber
parent bca72036a8
commit 478c3f5e8b
1 changed files with 35 additions and 5 deletions
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40
var/spack/repos/builtin/packages/augustus/package.py
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@ -11,17 +11,26 @@ class Augustus(MakefilePackage):
genomic sequences""" genomic sequences"""
homepage = "http://bioinf.uni-greifswald.de/augustus/" homepage = "http://bioinf.uni-greifswald.de/augustus/"
url = "http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.3.1.tar.gz" url = "https://github.com/Gaius-Augustus/Augustus/archive/3.3.2.tar.gz"
list_url = "http://bioinf.uni-greifswald.de/augustus/binaries/old" # Releases have moved to github
version('3.3.1', '8363ece221c799eb169f47e545efb951') version('3.3.2', sha256='d09f972cfd88deb34b19b69878eb8af3bbbe4f1cde1434b69cedc2aa6247a0f2')
version('3.3', '93691d9aafc7d3d0e1adf31ec308507f') version('3.3.1', sha256='011379606f381ee21b9716f83e8a1a57b2aaa01aefeebd2748104efa08c47cab',
version('3.2.3', 'b8c47ea8d0c45aa7bb9a82626c8ff830') url='https://github.com/Gaius-Augustus/Augustus/archive/v3.3.1-tag1.tar.gz')
version('3.3', '93691d9aafc7d3d0e1adf31ec308507f',
url='http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.3.tar.gz')
version('3.2.3', 'b8c47ea8d0c45aa7bb9a82626c8ff830',
url='http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.2.3.tar.gz')
depends_on('bamtools') depends_on('bamtools')
depends_on('gsl') depends_on('gsl')
depends_on('boost') depends_on('boost')
depends_on('zlib') 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('tabix', when='@3.3.1:')
depends_on('curl', when='@3.3.1:')
def edit(self, spec, prefix): def edit(self, spec, prefix):
with working_dir(join_path('auxprogs', 'filterBam', 'src')): with working_dir(join_path('auxprogs', 'filterBam', 'src')):
@ -52,6 +61,27 @@ def edit(self, spec, prefix):
makefile.filter('LIBS = -lbamtools -lz', makefile.filter('LIBS = -lbamtools -lz',
'LIBS = $(BAMTOOLS)/lib/bamtools' 'LIBS = $(BAMTOOLS)/lib/bamtools'
'/libbamtools.a -lz') '/libbamtools.a -lz')
with working_dir(join_path('auxprogs', 'bam2wig')):
makefile = FileFilter('Makefile')
# point tools to spack installations
bcftools = self.spec['bcftools'].prefix.include
samtools = self.spec['samtools'].prefix.include
htslib = self.spec['htslib'].prefix.include
tabix = self.spec['tabix'].prefix.include
makefile.filter('SAMTOOLS=.*$',
'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',
'$(SAMTOOLS)/../lib/libbam.a', string=True)
makefile.filter('$(HTSLIB)/libhts.a',
'$(HTSLIB)/../lib/libhts.a', string=True)
def install(self, spec, prefix): def install(self, spec, prefix):
install_tree('bin', join_path(self.spec.prefix, 'bin')) install_tree('bin', join_path(self.spec.prefix, 'bin'))