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merenlab / anvio

An analysis and visualization platform for 'omics data
http://merenlab.org/software/anvio
GNU General Public License v3.0
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How to set a different temp dir? #616

Closed JBuongio closed 6 years ago

JBuongio commented 6 years ago

Hi Meren, I'm running anvi-script-FASTA-to-contigs-db on a metagenome assembly that has about 180,000 contigs and keep running out of disk space on my work station. Is there a way to change the temp dir so I don't have to fill up the local machine?

Thanks, Joy

meren commented 6 years ago

In general the default temp directories anvi'o uses can be overwritten by TMPDIR, TEMP or TMP environment variables.

Apart from that, you shouldn't be using anvi-script-FASTA-to-contigs-db unless you are doing a quick and dirty analysis.

Instead you can use anvi-script-reformat-fasta, anvi-gen-contigs-database, anvi-run-hmms programs separately to make sure you have full control for every step (that script does it all for you in a quick way).