augustus: add v3.4.0 and update package (#22879)
- add version 3.4.0
- add patch for bam2wig when version 3.4.0
- url format changed again, hopefully stable now
- added missing python dependency when version >3.3.1
- have older version compile with htslib, samtools ,bcftools
- new dependencies for version 3.4.0
- sqlite
- mysql-client
- mysqlpp
- lp-solve
- suite-sparse
- refactored filtering code
- set python interpreter in scripts
This commit is contained in:
Glenn Johnson
GitHub
parent
ce6a617706
commit
a276f9405c
@ -0,0 +1,23 @@
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--- a/auxprogs/bam2wig/Makefile 2020-12-11 09:40:21.000000000 -0600
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+++ b/auxprogs/bam2wig/Makefile 2021-04-07 15:20:59.573957969 -0500
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@@ -19,18 +19,8 @@
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SOURCES = $(PROGRAM)
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OBJECTS = $(SOURCES:.c=.o)
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-ifneq ($(wildcard ${TOOLDIR}/htslib/htslib/.),) # if TOOLDIR exists and contains htslib
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- INCLUDES=-I$(TOOLDIR)/htslib -I$(TOOLDIR)/htslib/htslib
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- HTSLIBS=-L$(TOOLDIR)/htslib -Wl,-rpath,$(TOOLDIR)/htslib -lhts -lcurses -lm -lz -lpthread -lcurl -lssl -lcrypto -lbz2 -llzma
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- HTSERRHINT="Check if the installed HTSlib is of version 1.10 or higher - see README.txt"
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-else
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- INCLUDES=-I/usr/include/htslib
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- HTSLIBS=-lhts -lz -lpthread
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- ifdef DEF_TOOLDIR
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- HTSERRHINT="There is no htslib folder in directory $(TOOLDIR) \n"
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- endif
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- HTSERRHINT:=$(HTSERRHINT)"Check if HTSlib is installed and of version 1.10 or higher - see README.txt"
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-endif
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+INCLUDES=-I$(HTSLIBDIR)/include/htslib
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+HTSLIBS=-L$(HTSLIBDIR)/lib -Wl,-rpath,$(HTSLIBDIR)/lib -lhts -lcurses -lm -lz -lpthread -lcurl -lssl -lcrypto -lbz2 -llzma
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CFLAGS:=-Wall -O2 $(CFLAGS)
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CC?=gcc
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@ -12,9 +12,10 @@ class Augustus(MakefilePackage):
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genomic sequences"""
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homepage = "http://bioinf.uni-greifswald.de/augustus/"
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url = "https://github.com/Gaius-Augustus/Augustus/archive/3.3.2.tar.gz"
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# Releases have moved to github
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url = "https://github.com/Gaius-Augustus/Augustus/archive/v3.3.4.tar.gz"
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# Releases have moved to github
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version('3.4.0', sha256='2c06cf5953da5afdce1478fa10fcd3c280a3b050f1b2367bf3e731d7374d9bb8')
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version('3.3.2', sha256='d09f972cfd88deb34b19b69878eb8af3bbbe4f1cde1434b69cedc2aa6247a0f2')
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version('3.3.1-tag1', sha256='011379606f381ee21b9716f83e8a1a57b2aaa01aefeebd2748104efa08c47cab',
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url='https://github.com/Gaius-Augustus/Augustus/archive/v3.3.1-tag1.tar.gz')
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@ -24,14 +25,24 @@ class Augustus(MakefilePackage):
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url='http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.2.3.tar.gz')
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depends_on('perl', type=('build', 'run'))
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depends_on('python', when='@3.3.1:', type=('build', 'run'))
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depends_on('bamtools')
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depends_on('gsl')
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depends_on('boost')
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depends_on('zlib')
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depends_on('htslib', when='@3.3.1:')
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depends_on('bcftools', when='@3.3.1:')
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depends_on('samtools', when='@3.3.1:')
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depends_on('htslib')
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depends_on('bcftools')
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depends_on('samtools')
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depends_on('curl', when='@3.3.1:')
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depends_on('sqlite', when='@3.4.0:')
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depends_on('mysql-client', when='@3.4.0:')
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depends_on('mysqlpp', when='@3.4.0:')
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depends_on('lp-solve', when='@3.4.0:')
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depends_on('suite-sparse', when='@3.4.0:')
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# Trying to use filter_file here got too complicated so use a patch with a
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# corresponding environment variable
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patch('bam2wig_Makefile.patch', when='@3.4.0:')
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def edit(self, spec, prefix):
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# Set compile commands for each compiler and
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@ -44,30 +55,42 @@ def edit(self, spec, prefix):
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self.spec['boost'].prefix.include),
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'src/subdir.mk', string=True)
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# Set compile commands to all makefiles.
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# Makefiles to set spack compiler over gcc/g++
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makefiles = [
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'auxprogs/aln2wig/Makefile',
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'auxprogs/bam2hints/Makefile',
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'auxprogs/bam2wig/Makefile',
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'auxprogs/checkTargetSortedness/Makefile',
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'auxprogs/compileSpliceCands/Makefile',
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'auxprogs/homGeneMapping/src/Makefile',
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'auxprogs/joingenes/Makefile',
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'src/Makefile'
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'src/Makefile',
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]
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if self.version < Version('3.4.0'):
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makefiles.append('auxprogs/checkTargetSortedness/Makefile')
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if self.version >= Version('3.4.0'):
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makefiles.extend([
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'auxprogs/filterBam/src/Makefile',
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'src/unittests/Makefile',
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])
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for makefile in makefiles:
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filter_file('gcc', spack_cc, makefile, string=True)
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filter_file('g++', spack_cxx, makefile, string=True)
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bamtools = self.spec['bamtools'].prefix
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bcftools = self.spec['bcftools'].prefix
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htslib = self.spec['htslib'].prefix
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samtools = self.spec['samtools'].prefix
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with working_dir(join_path('auxprogs', 'filterBam', 'src')):
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makefile = FileFilter('Makefile')
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makefile.filter('BAMTOOLS = .*', 'BAMTOOLS = %s' % self.spec[
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'bamtools'].prefix)
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makefile.filter('BAMTOOLS = .*', 'BAMTOOLS = {0}'.format(bamtools))
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makefile.filter('INCLUDES = *',
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'INCLUDES = -I$(BAMTOOLS)/include/bamtools ')
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if 'bamtools@2.5:' in spec:
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makefile.filter('LIBS = -lbamtools -lz',
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'LIBS = $(BAMTOOLS)/lib64/'
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'LIBS = $(BAMTOOLS)/lib64'
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'/libbamtools.a -lz')
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if 'bamtools@:2.4' in spec:
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makefile.filter('LIBS = -lbamtools -lz',
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@ -75,39 +98,57 @@ def edit(self, spec, prefix):
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'/libbamtools.a -lz')
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with working_dir(join_path('auxprogs', 'bam2hints')):
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makefile = FileFilter('Makefile')
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makefile.filter('# Variable definition',
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'BAMTOOLS = %s' % self.spec['bamtools'].prefix)
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makefile.filter('INCLUDES = /usr/include/bamtools',
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'INCLUDES = $(BAMTOOLS)/include/bamtools')
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makefile.filter('/usr/include/bamtools',
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'{0}/include/bamtools'.format(bamtools))
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if 'bamtools@2.5:' in spec:
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makefile.filter('LIBS = -lbamtools -lz',
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'LIBS = $(BAMTOOLS)/lib64/'
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'/libbamtools.a -lz')
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'LIBS = {0}/lib64'
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'/libbamtools.a -lz'.format(bamtools))
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if 'bamtools@:2.4' in spec:
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makefile.filter('LIBS = -lbamtools -lz',
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'LIBS = $(BAMTOOLS)/lib/bamtools'
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'/libbamtools.a -lz')
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with working_dir(join_path('auxprogs', 'bam2wig')):
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makefile = FileFilter('Makefile')
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# point tools to spack installations
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if 'bcftools' in spec:
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bcftools = self.spec['bcftools'].prefix.include
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makefile.filter('BCFTOOLS=.*$',
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'BCFTOOLS=%s' % bcftools)
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if 'samtools' in spec:
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samtools = self.spec['samtools'].prefix.include
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makefile.filter('SAMTOOLS=.*$',
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'SAMTOOLS=%s' % samtools)
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if 'htslib' in spec:
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htslib = self.spec['htslib'].prefix.include
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makefile.filter('HTSLIB=.*$',
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'HTSLIB=%s' % htslib)
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'LIBS = {0}/lib/bamtools'
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'/libbamtools.a -lz'.format(bamtools))
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# fix bad linking dirs
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makefile.filter('$(SAMTOOLS)/libbam.a',
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'$(SAMTOOLS)/../lib/libbam.a', string=True)
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makefile.filter('$(HTSLIB)/libhts.a',
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'$(HTSLIB)/../lib/libhts.a', string=True)
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if self.version < Version('3.4.0'):
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with working_dir(join_path('auxprogs', 'bam2wig')):
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makefile = FileFilter('Makefile')
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# point tools to spack installations
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makefile.filter('BCFTOOLS=.*$',
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'BCFTOOLS={0}/include'.format(bcftools))
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makefile.filter('SAMTOOLS=.*$',
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'SAMTOOLS={0}/include'.format(samtools))
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makefile.filter('HTSLIB=.*$',
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'HTSLIB={0}/include'.format(htslib))
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# fix bad linking dirs
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makefile.filter('$(SAMTOOLS)/libbam.a',
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'$(SAMTOOLS)/../lib/libbam.a', string=True)
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makefile.filter('$(HTSLIB)/libhts.a',
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'$(HTSLIB)/../lib/libhts.a', string=True)
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with working_dir(join_path('auxprogs', 'checkTargetSortedness')):
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makefile = FileFilter('Makefile')
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makefile.filter('SAMTOOLS.*=.*$',
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'SAMTOOLS={0}/include'.format(samtools))
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makefile.filter('LIBS=-lbam',
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'LIBS=$(SAMTOOLS)/../lib/libbam.a',
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string=True)
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else:
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mysql = self.spec['mysql-client'].prefix
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mysqlpp = self.spec['mysqlpp'].prefix
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lpsolve = self.spec['lp-solve'].prefix
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with working_dir('src'):
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makefile = FileFilter('Makefile')
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makefile.filter(r'/usr/include/mysql\+\+',
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'{0}/include/mysql++'.format(mysqlpp))
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if '^mariadb-c-client' in spec:
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makefile.filter('/usr/include/mysql',
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'{0}/include/mariadb'.format(mysql))
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else:
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makefile.filter('/usr/include/mysql',
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'{0}/include/mysql'.format(mysql))
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makefile.filter('/usr/include/lpsolve',
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'{0}/include/lpsolve'.format(lpsolve))
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def install(self, spec, prefix):
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install_tree('bin', join_path(self.spec.prefix, 'bin'))
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@ -117,12 +158,22 @@ def install(self, spec, prefix):
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@run_after('install')
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def filter_sbang(self):
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with working_dir(self.prefix.scripts):
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pattern = '^#!.*/usr/bin/perl'
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pattern = '^#!.*'
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repl = '#!{0}'.format(self.spec['perl'].command.path)
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files = glob.iglob("*.pl")
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files = glob.glob("*.pl")
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for file in files:
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filter_file(pattern, repl, *files, backup=False)
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repl = '#!{0}'.format(self.spec['python'].command.path)
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files = glob.glob("*.py")
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for file in files:
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filter_file(pattern, repl, *files, backup=False)
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def setup_build_environment(self, env):
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if self.version >= Version('3.4.0'):
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htslib = self.spec['htslib'].prefix
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env.set('HTSLIBDIR', htslib)
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def setup_run_environment(self, env):
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env.set('AUGUSTUS_CONFIG_PATH', join_path(
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self.prefix, 'config'))
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