HPC command line - temporary directory

[Matilde-Rossi]

Hello ! I need to use the command found here: https://gatk.broadinstitute.org/hc/en-us/articles/360040509751-GenotypeGVCFs

My question is for this parameter: --tmp-dir=/path/to/large/tmp
"The command line argument --tmp-dir can be used to specify an alternate temperary storage location with sufficient space."

How do I set a temporary directory ?

[valegiunchiglia]

Hi! For what I understand, if you give a path after the command --tmp-dir then essentially a directory with the name you assigned will be created while your command is running. This directory will be then deleted once the command is done.
So for example, let's say that you set --tmp-dir \path\temporary_directory , this means that while your command runs the folder temporary_directory will be created in the path you gave. This will be then deleted once the command is done.

So essentially just try to set --tmp-dir \path\temporary_directory while you run the command, and that should be all you need to do.