Question: Galaxy temporary file
0
gravatar for snehalbpatil87
2.7 years ago by
snehalbpatil8730 wrote:

Hello :

Does anyone know how to create temporary files in the Galaxy ? For now I am using hidden tag for the output files .But those files will remain in the history. Is there any way to tag files in Galaxy so that it will delete those files after the job analysis.

Thanks Snehal

galaxy temparary files • 803 views
ADD COMMENTlink modified 2.7 years ago by Jennifer Hillman Jackson25k • written 2.7 years ago by snehalbpatil8730

Hi Snehal

Are you interested in those hidden files? Do you look at them to check and/or confirm the output?

If not:

  • you can work with 'real' temporary files, eg: https://docs.python.org/2/library/tempfile.html, http://perldoc.perl.org/File/Temp.html

  • or just use a fixed filename, eg: mytool $input1 $output1 tempfile . The tool will be executed in a temporary directory abyway (see the "job_working_directory" setting in the galaxy.ini file), which will be removed after the job completes (well, this depends on the setting for "cleanup_job" in the galaxy.ini file).

Hans-Rudolf

ADD REPLYlink written 2.7 years ago by Hotz, Hans-Rudolf1.8k
1
gravatar for Jennifer Hillman Jackson
2.7 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

If you are using a workflow, then the Output cleanup function will remove intermediate files per tool.

To use, open the workflow editor, click on a tool, then find the option in the far right panel:

Output cleanup

Hopefully this helps, Jen, Galaxy team

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 169 users visited in the last hour