$TAXONKIT_DB variable for file locations?

shenwei356 / taxonkit

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

https://bioinf.shenwei.me/taxonkit

MIT License

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Closed tseemann closed 5 years ago

tseemann commented 5 years ago

And copy "names.dmp" and "nodes.dmp" to data directory: "$HOME/.taxonkit".

We use taxonkit on a shared server with many users.

Would you be able to honour an env variable like $TAXONKIT_DB so that we can put the files in one place that's not a home directory?

Then we can have global export TAXONKIT_DB=/opt/data/taxonkit/ and the two files will be found there?

We'd rather not set global aliases for --names-file and --nodes-file

shenwei356 commented 5 years ago

Sure, I'll implement this in few days.

shenwei356 commented 5 years ago

Dear @tseemann , please test it. v0.2.5-dev4