Question: Galaxy temporary file
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snehalbpatil87 • 30 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
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modified 2.7 years ago
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Jennifer Hillman Jackson ♦ 25k
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2.7 years ago by
snehalbpatil87 • 30
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