mention that TMPDIR must be set

kundajelab / atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline

BSD 3-Clause "New" or "Revised" License

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mention that TMPDIR must be set #55

Closed antonkratz closed 7 years ago

antonkratz commented 7 years ago

Sugggestion, the installation instructions should mention that the shell variable TMPDIR must be set (I am not sure to where, I just set it to /tmp in my .bashrc and it seems to work). If it is not set - and by default it is not set in some fresh installations of Ubuntu/CentOS - the pipeline will crash. I think this is related to commit a6f7fabd4d36bfb200a3d9510ffd3d3cec548f21.

leepc12 commented 7 years ago

Thanks for reporting this. It's fixed in 02f55b5. If $TMPDIR is not set, the pipeline will ignore it.