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Run mothur tools with docker_enabled #1484

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cat-bro opened this issue Sep 5, 2023 · 2 comments
Open

Run mothur tools with docker_enabled #1484

cat-bro opened this issue Sep 5, 2023 · 2 comments

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@cat-bro
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cat-bro commented Sep 5, 2023

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
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cat-bro commented Sep 12, 2023

#1484

@cat-bro
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cat-bro commented Apr 3, 2024

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

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@cat-bro