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Add TMPDIR workaround for jbrowse text-index

Open cmdcolin opened this issue 1 year ago • 0 comments
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@SamCT ran into an issue running jbrowse text-index on his machine where one of the larger GFF would produce an error: EPIPE without much other info. I diagnosed this to a problem where the tmp directory was probably out of space, or otherwise limited in some way.

We could modify jbrowse text-index to catch generic EPIPE errors and suggest a TMPDIR workaround, which essentially looks like this

mkdir newdir
TMPDIR=newdir jbrowse text-index ...

that way, it will use the local newdir folder, which may have more space and resources, instead of the default /tmp

cmdcolin avatar Feb 06 '24 16:02 cmdcolin