# 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) import glob from spack import * class Augustus(MakefilePackage): """AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences""" homepage = "https://bioinf.uni-greifswald.de/augustus/" 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') 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('python', when='@3.3.1:', type=('build', 'run')) depends_on('bamtools') depends_on('gsl') depends_on('boost') depends_on('zlib') 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 # 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) # Makefiles to set spack compiler over gcc/g++ makefiles = [ 'auxprogs/aln2wig/Makefile', 'auxprogs/bam2hints/Makefile', 'auxprogs/bam2wig/Makefile', 'auxprogs/compileSpliceCands/Makefile', 'auxprogs/homGeneMapping/src/Makefile', 'auxprogs/joingenes/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 = {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' '/libbamtools.a -lz') if 'bamtools@:2.4' in spec: makefile.filter('LIBS = -lbamtools -lz', 'LIBS = $(BAMTOOLS)/lib/bamtools' '/libbamtools.a -lz') with working_dir(join_path('auxprogs', 'bam2hints')): makefile = FileFilter('Makefile') makefile.filter('/usr/include/bamtools', '{0}/include/bamtools'.format(bamtools)) if 'bamtools@2.5:' in spec: makefile.filter('LIBS = -lbamtools -lz', 'LIBS = {0}/lib64' '/libbamtools.a -lz'.format(bamtools)) if 'bamtools@:2.4' in spec: makefile.filter('LIBS = -lbamtools -lz', 'LIBS = {0}/lib/bamtools' '/libbamtools.a -lz'.format(bamtools)) if self.version < Version('3.4.0'): with working_dir(join_path('auxprogs', 'bam2wig')): makefile = FileFilter('Makefile') # point tools to spack installations makefile.filter('BCFTOOLS=.*$', 'BCFTOOLS={0}/include'.format(bcftools)) makefile.filter('SAMTOOLS=.*$', 'SAMTOOLS={0}/include'.format(samtools)) makefile.filter('HTSLIB=.*$', '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 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')) 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 = '^#!.*' repl = '#!{0}'.format(self.spec['perl'].command.path) 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')) env.prepend_path('PATH', join_path(self.prefix, 'scripts'))