diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/augustus/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/augustus/package.py | 129 |
1 files changed, 90 insertions, 39 deletions
diff --git a/var/spack/repos/builtin/packages/augustus/package.py b/var/spack/repos/builtin/packages/augustus/package.py index f105674261..4ad9991493 100644 --- a/var/spack/repos/builtin/packages/augustus/package.py +++ b/var/spack/repos/builtin/packages/augustus/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2021 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) @@ -12,9 +12,10 @@ class Augustus(MakefilePackage): 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 + url = "https://github.com/Gaius-Augustus/Augustus/archive/v3.3.4.tar.gz" + # Releases have moved to github + version('3.4.0', sha256='2c06cf5953da5afdce1478fa10fcd3c280a3b050f1b2367bf3e731d7374d9bb8') 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') @@ -24,14 +25,24 @@ class Augustus(MakefilePackage): url='http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.2.3.tar.gz') depends_on('perl', type=('build', 'run')) + depends_on('python', when='@3.3.1:', 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('htslib') + depends_on('bcftools') + depends_on('samtools') depends_on('curl', when='@3.3.1:') + depends_on('sqlite', when='@3.4.0:') + depends_on('mysql-client', when='@3.4.0:') + depends_on('mysqlpp', when='@3.4.0:') + depends_on('lp-solve', when='@3.4.0:') + depends_on('suite-sparse', when='@3.4.0:') + + # Trying to use filter_file here got too complicated so use a patch with a + # corresponding environment variable + patch('bam2wig_Makefile.patch', when='@3.4.0:') def edit(self, spec, prefix): # Set compile commands for each compiler and @@ -44,30 +55,42 @@ class Augustus(MakefilePackage): self.spec['boost'].prefix.include), 'src/subdir.mk', string=True) - # Set compile commands to all makefiles. + # Makefiles to set spack compiler over gcc/g++ 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' + 'src/Makefile', ] + if self.version < Version('3.4.0'): + makefiles.append('auxprogs/checkTargetSortedness/Makefile') + + if self.version >= Version('3.4.0'): + makefiles.extend([ + 'auxprogs/filterBam/src/Makefile', + 'src/unittests/Makefile', + ]) + for makefile in makefiles: filter_file('gcc', spack_cc, makefile, string=True) filter_file('g++', spack_cxx, makefile, string=True) + bamtools = self.spec['bamtools'].prefix + bcftools = self.spec['bcftools'].prefix + htslib = self.spec['htslib'].prefix + samtools = self.spec['samtools'].prefix + with working_dir(join_path('auxprogs', 'filterBam', 'src')): makefile = FileFilter('Makefile') - makefile.filter('BAMTOOLS = .*', 'BAMTOOLS = %s' % self.spec[ - 'bamtools'].prefix) + makefile.filter('BAMTOOLS = .*', 'BAMTOOLS = {0}'.format(bamtools)) makefile.filter('INCLUDES = *', 'INCLUDES = -I$(BAMTOOLS)/include/bamtools ') if 'bamtools@2.5:' in spec: makefile.filter('LIBS = -lbamtools -lz', - 'LIBS = $(BAMTOOLS)/lib64/' + 'LIBS = $(BAMTOOLS)/lib64' '/libbamtools.a -lz') if 'bamtools@:2.4' in spec: makefile.filter('LIBS = -lbamtools -lz', @@ -75,39 +98,57 @@ class Augustus(MakefilePackage): '/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') + makefile.filter('/usr/include/bamtools', + '{0}/include/bamtools'.format(bamtools)) if 'bamtools@2.5:' in spec: makefile.filter('LIBS = -lbamtools -lz', - 'LIBS = $(BAMTOOLS)/lib64/' - '/libbamtools.a -lz') + 'LIBS = {0}/lib64' + '/libbamtools.a -lz'.format(bamtools)) if 'bamtools@:2.4' in spec: makefile.filter('LIBS = -lbamtools -lz', - 'LIBS = $(BAMTOOLS)/lib/bamtools' - '/libbamtools.a -lz') - with working_dir(join_path('auxprogs', 'bam2wig')): - makefile = FileFilter('Makefile') - # point tools to spack installations - if 'bcftools' in spec: - bcftools = self.spec['bcftools'].prefix.include + 'LIBS = {0}/lib/bamtools' + '/libbamtools.a -lz'.format(bamtools)) + + if self.version < Version('3.4.0'): + with working_dir(join_path('auxprogs', 'bam2wig')): + makefile = FileFilter('Makefile') + # point tools to spack installations makefile.filter('BCFTOOLS=.*$', - 'BCFTOOLS=%s' % bcftools) - if 'samtools' in spec: - samtools = self.spec['samtools'].prefix.include + 'BCFTOOLS={0}/include'.format(bcftools)) makefile.filter('SAMTOOLS=.*$', - 'SAMTOOLS=%s' % samtools) - if 'htslib' in spec: - htslib = self.spec['htslib'].prefix.include + 'SAMTOOLS={0}/include'.format(samtools)) makefile.filter('HTSLIB=.*$', - 'HTSLIB=%s' % htslib) + 'HTSLIB={0}/include'.format(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) + with working_dir(join_path('auxprogs', 'checkTargetSortedness')): + makefile = FileFilter('Makefile') + makefile.filter('SAMTOOLS.*=.*$', + 'SAMTOOLS={0}/include'.format(samtools)) + makefile.filter('LIBS=-lbam', + 'LIBS=$(SAMTOOLS)/../lib/libbam.a', + string=True) + else: + mysql = self.spec['mysql-client'].prefix + mysqlpp = self.spec['mysqlpp'].prefix + lpsolve = self.spec['lp-solve'].prefix - # 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) + with working_dir('src'): + makefile = FileFilter('Makefile') + makefile.filter(r'/usr/include/mysql\+\+', + '{0}/include/mysql++'.format(mysqlpp)) + if '^mariadb-c-client' in spec: + makefile.filter('/usr/include/mysql', + '{0}/include/mariadb'.format(mysql)) + else: + makefile.filter('/usr/include/mysql', + '{0}/include/mysql'.format(mysql)) + makefile.filter('/usr/include/lpsolve', + '{0}/include/lpsolve'.format(lpsolve)) def install(self, spec, prefix): install_tree('bin', join_path(self.spec.prefix, 'bin')) @@ -117,12 +158,22 @@ class Augustus(MakefilePackage): @run_after('install') def filter_sbang(self): with working_dir(self.prefix.scripts): - pattern = '^#!.*/usr/bin/perl' + pattern = '^#!.*' repl = '#!{0}'.format(self.spec['perl'].command.path) - files = glob.iglob("*.pl") + files = glob.glob("*.pl") for file in files: filter_file(pattern, repl, *files, backup=False) + repl = '#!{0}'.format(self.spec['python'].command.path) + files = glob.glob("*.py") + for file in files: + filter_file(pattern, repl, *files, backup=False) + + def setup_build_environment(self, env): + if self.version >= Version('3.4.0'): + htslib = self.spec['htslib'].prefix + env.set('HTSLIBDIR', htslib) + def setup_run_environment(self, env): env.set('AUGUSTUS_CONFIG_PATH', join_path( self.prefix, 'config')) |