UCSF-Costello-Lab / LG3_Pipeline

The original LG3 pipeline
https://github.com/UCSF-Costello-Lab/LG3_Pipeline
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Make Java respect TMPDIR #172

Open HenrikBengtsson opened 2 years ago

HenrikBengtsson commented 2 years ago

Issue

It turns out Java completely ignores the TMPDIR environment variable. Instead, it's hardcoded to use /tmp as the temporary drive (argh!). If /tmp is small, there's a great risk for filling it up, especially so if there are multiple Java processes running on the same machine.

Solution

Make sure to use the following everywhere we use Java in the LG3 pipeline:

java -Djava.io.tmpdir="${TMPDIR:-/tmp}" ...