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biocore-ntnu / epic

(DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER
http://bioepic.readthedocs.io
MIT License
31 stars 6 forks source link

Temporary Directory #39

Closed c-guzman closed 7 years ago

c-guzman commented 7 years ago

I'm running to a problem where my /tmp folder is running out of space during a pipeline run. I was wondering if there was an option to choose where temporary files are stored for epic?

endrebak commented 7 years ago

Thanks for reporting this. I had no idea this could happen. I do not use the tmp folder myself, but I guess unix sort does. Do you have a log of all the output messages when you got the error? This would help me understand where it happened.

c-guzman commented 7 years ago

I think this is less of a specific EPIC problem, and more of a general case problem where there are too many programs that store temporary files in the /tmp directory (macs2, epic, deeptools, etc) that don't allow for a change in directory for storing temp files. With enough processes running at one time, the /tmp file gets filled over. Theres currently a issue in the MACS2 github about the same thing.

endrebak commented 7 years ago

The only thing that uses a tmpdir in my software is the unix sort command. If you want to change the tmpdir when running epic you can do TMPDIR="your/temp/folder" && epic -h. Modern versions of sort should respond to the $TMPDIR variable.