kymata-atlas / kymata-core

Core Kymata codebase, including statistical analysis and plotting tools
https://kymata.org
MIT License
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Remove hardcoding of kymata-toolbox directory in submit_gridsearch.sh #142

Open neukym opened 10 months ago

neukym commented 10 months ago

@caiw tried to fix it with

# This gets the directory of the toolbox, assuming that *this file you're reading right now* is in the root directory of
# the toolbox
TOOLBOX_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )

but we get this

'/usr/bin/bash: line 1: cd: /var/spool/slurm/job3347806: No such file or directory'

So I put it back to hardcoded. It must be that the SLURM thinks it is in '/var/spool/slurm/job3347806' when it runs...

caiw commented 10 months ago

Ah, that's annoying.

One way to fix this would be to have a python script which builds the job-submission string on the fly. I.e. the python toolbox gets its own location and injects that into the shell script.

Note to self: I've done this before using a job submit function and a shell shim.

caiw commented 10 months ago

Not high priority though.

neukym commented 10 months ago

Agreed - let's put this on hold for a bit.