How to set TMP directory in Galaxy jobs

Hi all,

We have a local Galaxy deployed in our servers and we are using Sun Grig Engine as the job runner. When running big files using BWA-MEM2 Galaxy workflow, we are getting the following error:

failed to create temporary file “/tmp/181.1.all.q/samtools.30529.6025.tmp.0029.bam” : No space left on device

Looking form more info, I have seen that /tmp file has only 10GB available and we want to move its location to a bigger disk. We have tried to declare the environment variable TMPDIR and to configure job_conf.xml as commented in this issue: Improved home and temp directory handling. by jmchilton · Pull Request #5193 · galaxyproject/galaxy · GitHub but this have not worked.

Are we missing something about this configuration?
How can we set the tmp directory location for running jobs?

Thanks in advance,

Paco

Welcome, @fcasnun

That change went into effect in the 23.0 release with some deployment specific tuning happening in 23.1. Which are you running? Does that explain what you are seeing?

Release details (see Fixes)

Then the docs have a note here with links to more

Please let us know if that helps or not, and we can followup more! :hammer_and_wrench:

Thanks for the help @jennaj . I am using currently Galaxy v.24. I have solved the problem by modifying the job_conf.file, adding a parameter in the destination section called tmp_dir with the actual value of the tmp directory needed

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