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Adding tpv variable for cooler_cload_tabix tool #1368

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merged 5 commits into from
Nov 28, 2024
Merged

Adding tpv variable for cooler_cload_tabix tool #1368

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d0c27a0
Adding tpv variable for cooler_cload_tabix tool
SaimMomin12 Nov 28, 2024
ab497c2
Fix linting
SaimMomin12 Nov 28, 2024
5a65d85
Fix linting (2)
SaimMomin12 Nov 28, 2024
92f5773
add HDF5_USE_FILE_LOCKING ENV and set it to false in TPV tool defaults
sanjaysrikakulam Nov 28, 2024
c7af9b3
Add the singularity ENV SINGULARITYENV_HDF5_USE_FILE_LOCKING to tool …
sanjaysrikakulam Nov 28, 2024
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5 changes: 4 additions & 1 deletion files/galaxy/tpv/tool_defaults.yml
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Expand Up @@ -8,7 +8,10 @@ tools:
mem: cores * 3.8
gpus: 0
env:
GALAXY_MEMORY_MB: "{int(mem * 1024)}" # set 5/2023 might be moved to runner or tool wrappers, related to Galaxy issue 15952
- name: GALAXY_MEMORY_MB
value: "{int(mem * 1024)}" # set 5/2023 might be moved to runner or tool wrappers, related to Galaxy issue 15952
- name: HDF5_USE_FILE_LOCKING
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value: "FALSE"
params:
metadata_strategy: "extended"
tmp_dir: true
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5 changes: 0 additions & 5 deletions files/galaxy/tpv/tools.yml
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Expand Up @@ -207,11 +207,6 @@ tools:
prefer:
- condor-tpv

toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/.*:
env:
- name: HDF5_USE_FILE_LOCKING
value: "FALSE"

toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/.*:
rules:
- if: input_size >= 0.01
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