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freebayes: Dynamic memory allocation
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Most freebayes jobs have inputs smaller than 10GB and use less than 15GB of memory, rather than the 90GB that are currently being requested.

Since UseGalaxy.eu resubmits jobs up to two times when they run out of memory, tripling the memory request each time, this change should cover about 99% of jobs within two resubmissions (see the graph in PR #881).
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kysrpex committed Aug 31, 2023
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3 changes: 3 additions & 0 deletions files/galaxy/tpv/tools.yml
Original file line number Diff line number Diff line change
Expand Up @@ -688,6 +688,9 @@ tools:
- if: input_size >= 25
fail: Too much data, please check if the input is correct.

toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/.*:
mem: 9 + input_size * 1

toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/.*:
inherits: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/.*

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