zhangyiss/spack
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

augustus: Set compile commands for each compiler and Fix for using 'boost' on Spack (#13975)

Browse Source 
* 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
This commit is contained in:
t-karatsu 2019-12-07 03:39:23 +09:00 committed by Adam J. Stewart
parent 5d523dd689
commit 06042ec7ec
1 changed files with 25 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

25
var/spack/repos/builtin/packages/augustus/package.py
View File

@ -84,6 +84,31 @@ def edit(self, spec, prefix):
makefile.filter('$(HTSLIB)/libhts.a', makefile.filter('$(HTSLIB)/libhts.a',
'$(HTSLIB)/../lib/libhts.a', string=True) '$(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): def install(self, spec, prefix):
install_tree('bin', join_path(self.spec.prefix, 'bin')) install_tree('bin', join_path(self.spec.prefix, 'bin'))
install_tree('config', join_path(self.spec.prefix, 'config')) install_tree('config', join_path(self.spec.prefix, 'config'))