Improve build process #237
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change boost install method remove travis_retry change boost build dir add boost root to cmake WIP: trying to get cmake building WIP: dont rely on previous CMAKE_OPTIONS variable WIP: add missing boost variables to script WIP: fiddling with boost root WIP: comment out cache WIP: try and make boost install simpler WIP: trying to get pandora to include boost WIP: try to install boost in /usr WIP: add sudo WIP: fix ctest verbose flag WIP: try and cache boost WIP: format readme and update travis badges WIP: remove caching of /usr dirs
leoisl
approved these changes
Oct 30, 2020
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I had just one very minor comment, so I am approving these changes directly. You can address or reject this minor comment, all is fine by me! In summary:
- Improvements to the CI and build process are amazing and really needed;
- The code cleaning you did will improve our post-paper development QOL so much, can't thank you enough!
- Very happy to see that all messages now go to the logging object, with the proper logging level;
Thanks a lot for this!
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DISCLAIMER: don't let the number of file changes put you off - I just deleted a lot of comments...
Added
--clean-dbgflag inpandora discover. This exposes the option for cleaning the GATB de Bruijn graph before doing local assembly.Removed
coutorcerrChanged
--discover-kparameter to only accept integers in the range [0-32) as a guard for this. I also streamlined the cmake build process for GATB to build from a git commit rather than downloading a tar ball. This is so that we can easily transition to a fork of GATB if we need to to support multithreading.std::coutandstd::cerrhas been replaced with writes to the log instead [closes Logging should go to stderr #221]--merge-distis now 15 [Acceptable local assembly performance #74 and Filter pandora map VCFs mbhall88/head_to_head_pipeline#48 will have evidence to support this change soon]