Issues/3916 export all slurm

[Hexotical]

Changelog Entry

To be copied to the draft changelog by merger:

Make --export-all the default for slurm arguments

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[adamnovak]

This would fix #3916.

[adamnovak]

@Hexotical Do you want to finish this PR?

[thiagogenez]

Hi @adamnovak
I was about to do a PR regarding this issue (https://github.com/DataBiosphere/toil/issues/3916) of adding/appending ALL to --export.

Is this PR will be merged soon? I help to finalise if you need a hand. Cheers

[adamnovak]

@thiagogenez We're hoping to merge this as soon as we can get it working, thanks for the help!

Really for this you would want to talk to @Hexotical and not me, though; it looks like we forgot to set the assignee on #3916 but we kind of gave the issue to him to do.

And yeah, docker exec export is never going to work, because exec starts a new process and export is a Bash builtin to set an environment variable for itself. AFAIK only the process itself can set an environment variable on a running process.

[thiagogenez]

@thiagogenez We're hoping to merge this as soon as we can get it working, thanks for the help!

Really for this you would want to talk to @Hexotical and not me, though; it looks like we forgot to set the assignee on #3916 but we kind of gave the issue to him to do.

And yeah, docker exec export is never going to work, because exec starts a new process and export is a Bash builtin to set an environment variable for itself. AFAIK only the process itself can set an environment variable on a running process.

Thank you @adamnovak for the message. Glad to help with this. I'm very interested to test Toil on Slurm using Cactus.

Please @Hexotical count on me if you need a hand for testing etc.