Add requirements for the Galaxy-ME tools #77
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tools.yml
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| toolshed.g2.bx.psu.edu/repos/guerler/charts/charts/.*: | ||
| mem: 10 | ||
| toolshed.g2.bx.psu.edu/repos/hammock/hammock/hammock_1.0/.*: | ||
| mem: 20 | ||
| env: | ||
| _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G | ||
| toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/.*: | ||
| cores: 12 | ||
| mem: 128 |
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This seems to be a lot, is this really needed? Is this dependent on the input size?
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I guess you haven't seen mesmer yet...
As I mentioned in the initial comment, the values come from the cancer.usegalaxy.org instance where the tools run correctly. So I figured we start there and bring it down if possible once we have some runtime data?
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We do have this tool installed:
(venv) galaxy@sn06:~$ gxadmin tsvquery tool-metrics %ip_convertimage% memory.max_usage_in_bytes --like | awk '{print $1 / 1024 / 1024 / 1024}' | gxadmin filter histogram
( 0.114, 22.214) n=1433 **************************************************
[ 22.214, 44.314) n=6
[ 44.314, 66.415) n=20
[ 66.415, 88.515) n=1
[ 88.515, 110.615) n=7
[ 110.615, 132.716) n=1
[ 132.716, 154.816) n=0
[ 154.816, 176.916) n=0
[ 176.916, 199.017) n=0
[ 199.017, 221.117) n=1
[ 221.117, 243.218) n=0
[ 243.218, 265.318) n=0
[ 265.318, 287.418) n=0
[ 287.418, 309.519) n=0
[ 309.519, 331.619) n=0
[ 331.619, 353.719) n=0
[ 353.719, 375.820) n=0
[ 375.820, 397.920) n=0
[ 397.920, 420.021) n=0
[ 420.021, 442.121) n=0
[ 442.121, 464.221) n=0
[ 464.221, 486.322) n=0
[ 486.322, 508.422) n=0
[ 508.422, 530.522) n=1
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OK, nice. So do you think we should go with 64GB or bring it all the way down to 24?
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At least this is what data suggesting, maybe you have large inputs and it takes more mem? or it scales with cores? In that case we need to have a nice rule.
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I have no usage data atm so I'll just drop it to 30GB for the time being.
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Forgot I didn't actually update the config following my reply... Updated now.
This includes resource requirement for the Galaxy-ME tutorial: https://training.galaxyproject.org/training-material/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.html
Values come from the cancer.usegalaxy.org instance.