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galaxyproject / tpv-shared-database

A shared database of rules for Total Perspective Vortex used by the usegalaxy.* federation.
MIT License
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Update minimum RAM for Flye #55

Open diegomics opened 6 months ago

diegomics commented 6 months ago

Hi! To run, Flye needs to first get all the reads in the memory, therefore, the minimum RAM requirement equals the (uncompressed) reads file size. Would it be possible to modify the RAM to something like 1.2 times the reads file size? Now it is:

toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/.*:
  cores: 20
  mem: 60

:)

bgruening commented 5 months ago

You can define rules, similar to https://github.com/galaxyproject/tpv-shared-database/blob/main/tools.yml#L204

Or this example here: https://github.com/usegalaxy-eu/infrastructure-playbook/blob/master/files/galaxy/tpv/tools.yml#L695

You can also write more complex rules as we have done for hifiasm: https://github.com/usegalaxy-eu/infrastructure-playbook/blob/master/files/galaxy/tpv/tools.yml

nuwang commented 5 months ago

Thanks for pointing this out - it'll make a great example for the docs too. A spec like this should work:

toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/.*:
  cores: 20
  mem: min(input_size*1.2, 256)