[Bioperl-l] How put tmp file in the tmp directory when using Bio::Tools::Run::StandAloneBlastPlus?

Dave Messina David.Messina at sbc.su.se
Sun Jun 6 19:32:57 EDT 2010

> Is there a way to put the tmp files in a
> tmp directory say /tmp?

Hmm, that probably shouldn't be happening. And indeed, BioPerl modules use File::Temp, which creates temp files in /tmp (or the equivalent).

It's possible that it's a side effect of using Bio::Perl, which is composed of convenience methods for the beginner and is not really intended for serious use. For that reason, it may be writing in the current directory to minimize the possibility of write permissions errors which could be hard for a beginner to deal with. But that's only a guess.

If you use Bio::SeqIO directly instead of read_seq and write_seq, and if you're still seeing temp files in your current directory, please let us know.


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