Run mothur tools with docker_enabled

usegalaxy-au / infrastructure

Galaxy Australia's Ansible scripts

MIT License

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Run mothur tools with docker_enabled #1484

Open cat-bro opened 1 year ago

cat-bro commented 1 year ago

need to test whether this entry in tpv/tools.yml will work for all mothur tools including ones with specific entries. This will protect user data from large files created in error.

  toolshed.g2.bx.psu.edu/repos/iuc/mothur.*:
    params:
      docker_enabled: true
      docker_run_extra_arguments: --pids-limit 10000 --ulimit fsize=1000000000 --env TERM=vt100

cat-bro commented 12 months ago

https://github.com/usegalaxy-au/infrastructure/issues/1484

cat-bro commented 5 months ago

This does not work. the fsize limit is ~500GB and mothur jobs still have working directory files that exceed this.