diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/augustus/package.py | 50 |
1 files changed, 25 insertions, 25 deletions
diff --git a/var/spack/repos/builtin/packages/augustus/package.py b/var/spack/repos/builtin/packages/augustus/package.py index 1ed1b85f72..a99be82637 100644 --- a/var/spack/repos/builtin/packages/augustus/package.py +++ b/var/spack/repos/builtin/packages/augustus/package.py @@ -34,6 +34,31 @@ class Augustus(MakefilePackage): depends_on('curl', when='@3.3.1:') 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) + + # Set compile commands to all makefiles. + 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' + ] + for makefile in makefiles: + filter_file('gcc', spack_cc, makefile, string=True) + filter_file('g++', spack_cxx, makefile, string=True) + with working_dir(join_path('auxprogs', 'filterBam', 'src')): makefile = FileFilter('Makefile') makefile.filter('BAMTOOLS = .*', 'BAMTOOLS = %s' % self.spec[ @@ -84,31 +109,6 @@ class Augustus(MakefilePackage): makefile.filter('$(HTSLIB)/libhts.a', '$(HTSLIB)/../lib/libhts.a', string=True) - # 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) - - # Set compile commands to all makefiles. - 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' - ] - for makefile in makefiles: - filter_file('gcc', spack_cc, makefile, string=True) - filter_file('g++', spack_cxx, makefile, string=True) - def install(self, spec, prefix): install_tree('bin', join_path(self.spec.prefix, 'bin')) install_tree('config', join_path(self.spec.prefix, 'config')) |