added GALAXY_MEMORY_MB_PER_SLOT variable

[bernt-matthias]

When starting to use GALAXY_MEMORY_MB I realized that some tools want to know the total memory and some the memory per thread. I found it cumbersome if tool developers need to calculate that value in the tool script.

So here is my suggestion.

The two if statements may simplify the integration of statements for further cluster schedulers. Some seem to report total memory (apparently SLURM) and others per thread (UNIVA: #4857).

[jmchilton]

Ping @natefoo - any thoughts? Seems like an okay change to me.

[natefoo]

Yeah, seems reasonable. Just a minor request, can it be $GALAXY_MEMORY_MB_PER_SLOT instead?

[bernt-matthias]

renamed it.

[bernt-matthias]

Where could I add a bit of documentation for this?

[mvdbeek]

galaxy/lib/galaxy/tools/xsd/galaxy.xsd

Line 2659 in 0be36ef

``\$GALAXY_MEMORY_MB`` | Amount of memory in megabytes (1024^2 bytes) allocated by the administrator (via the resource manager) to the tool for the given job. If unset, tools should not attempt to limit memory usage.

seems like a good place

[bernt-matthias]

Maybe also add some more details here:

https://planemo.readthedocs.io/en/latest/writing_advanced.html#cluster-usage
https://galaxyproject.org/admin/config/galaxy_slots/

?

[natefoo]

Both those places seem like good candidates. The Hub page should probably move to docs.galaxyproject.org though.

[bernt-matthias]

@natefoo Is the docs docs.galaxyproject.org content also on github?

[nsoranzo]

It's generated from files in doc/source/ subdirectory of this repository.

[jmchilton]

Thanks again - this good stuff and updating documentation is such a great idea (I should try that for something I do someday - meh probably not).