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EddyRivasLab / easel

Sequence analysis library used by Eddy/Rivas lab code
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Set tmp directory for esl-sfetch #53

Closed arglog closed 3 years ago

arglog commented 3 years ago

Hi easel team,

I'm using esl-sfetch to build index for a large fasta file (metaclust_nr.fasta, 241G). I used the following command

esl-sfetch --index metaclust_nr.fasta

I got the following error. It seems there is no space available under /tmp

Creating SSI index for metaclust_nr.fasta...    sort: write failed: /tmp/sort5sUUWF: No space left on device

Failed to write keys to ssi file metaclust_nr.fasta.ssi:
  external sort of primary keys failed

As the /tmp on my machine wasn't mounted to a large drive, I'm wondering if I can specify another path to be used as the temp directory, so that esl-sfetch has enough space to write? I didn't find any argument for this purpose in esl-sfetch -h. Is there any walkaround?

Thanks!

cryptogenomicon commented 3 years ago

Yes, you can set ${TMPDIR} or ${TMP} in your shell environment to be the path to any directory you want. This is the usual UNIX/POSIX behavior, I believe!

arglog commented 3 years ago

Yes, export TMPDIR=/path/to/tmp solves the problem! Thanks!