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Trying with docker tmpfs mount #1254

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merged 6 commits into from
Jul 17, 2024
Merged

Trying with docker tmpfs mount #1254

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d86740b
trying with docker tmpfs mount
mira-miracoli Jul 9, 2024
871277e
Merge branch 'master' into tmp-tmp-fix
mira-miracoli Jul 9, 2024
026a601
set size and increse mem
mira-miracoli Jul 9, 2024
06763bd
inherit basic docker tool
mira-miracoli Jul 17, 2024
bcbce8c
remove scheduling
mira-miracoli Jul 17, 2024
32b9ff8
remove env
mira-miracoli Jul 17, 2024
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6 changes: 6 additions & 0 deletions files/galaxy/tpv/tools.yml
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Expand Up @@ -324,6 +324,10 @@ tools:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/artbio/manta/manta/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/goeckslab/squidpy/squidpy_spatial/*:
inherits: basic_docker_tool
params:
docker_run_extra_arguments: "--mount type=tmpfs,destination=/tmp"
toolshed.g2.bx.psu.edu/repos/goeckslab/gate_finder/gate_finder/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/goeckslab/vitessce_spatial/vitessce_spatial/.*:
Expand Down Expand Up @@ -1307,6 +1311,8 @@ tools:
toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/.*:
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cores: 8
mem: 40
params:
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docker_run_extra_arguments: "--mount type=tmpfs,destination=/tmp"
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env:
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SINGULARITY_WRITABLE_TMPFS: 1
rules:
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