Temp folder location

[quark-spec]

Dear developers,

I was running command-line philosopher pipeline and at some point was told a directory under /tmp could not be found. I was thinking if there is a way to set another directory as the temp folder. This doesn't happen every time and so far only occurs when the analysis takes quite a long time, which in this case is expected (I think) as it is a proteogenomics analysis and the database size is large.

Thank you.

[quark-spec]

I found there is a --temp parameter in the workspace command, but philosopher is still using /tmp as the temp folder after I gave it an alternative location.

[prvst]

Please see #261

[prvst]

Try removing the workspace manually, and set it again

[quark-spec]

Unfortunately didn't work. Philosopher is still using /tmp.

My command looks like this

/home/oscar/tools/philosopher-3.4.13/philosopher workspace --temp /home/oscar/Data/SY201217-DMS-5564/results/tmp
/home/oscar/tools/philosopher-3.4.13/philosopher workspace --init
/home/oscar/tools/philosopher-3.4.13/philosopher pipeline --config /home/oscar/Data/SY201217-DMS-5564/params/philosopher.yml BatchB

Is the command correct? Thank you.

[quark-spec]

I also tried this command

/home/oscar/tools/philosopher-3.4.13/philosopher workspace --init --temp /home/oscar/Data/SY201217-DMS-5564/results/tmp
/home/oscar/tools/philosopher-3.4.13/philosopher pipeline --config /home/oscar/Data/SY201217-DMS-5564/params/philosopher.yml BatchB

Same result - Philsoopher still using /tmp.

[quark-spec]

Removing the .meta folder and set again did not help

[prvst]

@quark-spec I'm going to investigate this for you

[prvst]

I just noticed that you're not using the latest version. Can you update the program and try again?

[quark-spec]

I would like to use the latest version as well, but this is part of a project that has been using v3.4.13 and we prefer not to change the software version for consistency's sake. Is it possible to fix it without updating Philosopher? Thank you.

[prvst]

Unfortunately, no. We can't amend or improve a previous version.

[quark-spec]

I am able to set the temp folder with philosopher 4.0.0. I am also wondering if there is an option to set the temp in FragPipe. Thank you.

[prvst]

Yes, you have to run it like this:

$ export JAVA_OPTS=-Djava.io.tmpdir=<your_preferred_tempdir>
$ <path_to_fragpipe>/fragpipe