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| author | t-karatsu <49965247+t-karatsu@users.noreply.github.com> | 2019-12-07 03:39:23 +0900 |
|---|---|---|
| committer | Adam J. Stewart <ajstewart426@gmail.com> | 2019-12-06 12:39:23 -0600 |
| commit | 06042ec7ec481721c59772aa33e8110acf5d076d (patch) | |
| tree | 112743fad0d77ed27c44794205aaaff9d29e8c49 | |
| parent | 5d523dd6890148af1cf18a04c312738d8c2dec26 (diff) | |
| download | spack-06042ec7ec481721c59772aa33e8110acf5d076d.tar.gz spack-06042ec7ec481721c59772aa33e8110acf5d076d.tar.bz2 spack-06042ec7ec481721c59772aa33e8110acf5d076d.tar.xz spack-06042ec7ec481721c59772aa33e8110acf5d076d.zip | |
augustus: Set compile commands for each compiler and Fix for using 'boost' on Spack (#13975)
* augustus: Set compile commands for each compiler and Fix for using 'boost' on Spack
* fix for flake8
* delete 'string' args
* Fix args of filter_file func
* Fix args of other filter_file func
| -rw-r--r-- | var/spack/repos/builtin/packages/augustus/package.py | 25 |
1 files changed, 25 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/augustus/package.py b/var/spack/repos/builtin/packages/augustus/package.py index c909ce102a..1ed1b85f72 100644 --- a/var/spack/repos/builtin/packages/augustus/package.py +++ b/var/spack/repos/builtin/packages/augustus/package.py @@ -84,6 +84,31 @@ 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')) |