So you want temp directories and working directories to sit on the external drive but not Galaxy's files:
Lets say this external disk is mounted as /mnt/gxwork. I would create two directories under that maybe /mnt/gxwork/tmp and /mnt/gxwork/working.
Setting the working directory is the easier part - you just need to set
job_working_directory = /mnt/gxwork/working
Ideally - where Galaxy tools write temporary files is handled outside of Galaxy - so if you could mount /tmp using that /mnt/gxwork/tmp directory it would be best. This isn't always realistic though. The alternative is to make sure all jobs run with TMP, TEMP, and TMPDIR environment variables set to that directory. There are a myriad of ways to do this that are going to depend on your configuration. In most cases - it is probably best to just place these definitions in your Galaxy users .bashrc file maybe - if you really want Galaxy to handle this I think you can setup an environment file and point the environment_setup_file option at it.
So create a galaxy_job_env file with following contents:
export TMP=/mnt/gxwork/tmp export TEMP=/mnt/gxwork/tmp export TMPDIR=/mnt/gxwork/tmp
and then set environment_setup_file in Galaxy's universe_wsgi.ini to point at it.
Some older tools will use - new_file_path in universe_wsgi.ini for temporary directories. So I would also point this at that /mnt/gxwork/working.
Hopefully this helps.
-John
On Wed, Aug 13, 2014 at 12:08 PM, Juan Vladimir de la Rosa Medina jvdelarosa@hotmail.com wrote:
Hi,
now I am trying to set the working and temp directories of Galaxy enviroment in a external drive, but I do not know how to do this task. I know that universe_wgsi.ini file has a section called Files and directories, with diferent options like job_working_directory, collect_outputs_from, file_path and new_file_path. However, I do not know if these are the options to be set or if there are other options. I also do not know how to set these options. Can anybody help me or point me to a tutorial?
Thanks
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