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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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13 changes: 9 additions & 4 deletions files/galaxy/tpv/tools.yml
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Expand Up @@ -324,6 +324,11 @@ 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
mem: 6
params:
docker_run_extra_arguments: "--mount type=tmpfs,tmpfs-size=2147483648,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 @@ -1305,17 +1310,17 @@ tools:
- singularity

toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/.*:
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inherits: basic_docker_tool
cores: 8
mem: 40
mem: 42
params:
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docker_run_extra_arguments: "--mount type=tmpfs,tmpfs-size=2147483648,destination=/tmp"
env:
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SINGULARITY_WRITABLE_TMPFS: 1
rules:
- id: funannotate_annotate_large_input
if: input_size > 3.2
mem: 62
scheduling:
require:
- singularity

toolshed.g2.bx.psu.edu/repos/iuc/funannotate_clean/funannotate_clean/.*:
cores: 8
Expand Down
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