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GATB / bcalm

compacted de Bruijn graph construction in low memory
MIT License
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Fails to build from source on ARM MacOS #78

Open fgindraud opened 6 months ago

fgindraud commented 6 months ago

While trying to help a user to build kissplice (which depends on bcalm) on an ARM Mac, I encountered two build issues. I managed to track them down and fix them using github actions CI, as I do not have access to any ARM Mac myself.

The first issue is a missing #include inside the hdf5 copy within gatb-core. This compiles fine on Linux but failed for newer ARM MacOS. The fix used for my tests is available at https://github.com/fgindraud/gatb-core/commit/4dffb1a995583aafefa1a1d576f18baea040a71e. I can create a pull request for it if you want.

The second issue is the same as the one fixed by https://github.com/GATB/gatb-core/commit/dc9264e20ec0c50cd8b82ecea300b2a397b823d7, but this has not been propagated to bcalm yet (gatb-core submodule points to an earlier commit).

Due to both problems being in gatb-core, the problems can be fixed by adding the first fix to gatb-core, then update the submodule within bcalm to get both fixes. I cannot provide a pull request directly for bcalm as the new commit must first exist in gatb-core to be able to update the submodule.

fgindraud commented 6 months ago

I found a way to make the pull requests in both gatb-core and bcalm that should work with submodules, as long as commit ids are not rewritten. The PR in bcalm requires the one in gatb-core first.