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openvax / pyensembl

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
Apache License 2.0
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Allow a custom cache directory #96

Closed tavinathanson closed 6 years ago

tavinathanson commented 9 years ago

datacache's envkey functionality should be surfaced to pyensembl so that users can customize the cache directory.

See https://github.com/hammerlab/varcode/issues/98

kippakers commented 9 years ago

+1 for this request. My home directory is capped at 10GB.

iskandr commented 9 years ago

@tavinathanson Should we add a pyensembl command like pyensembl set-cache-dir?

tavinathanson commented 9 years ago

@iskandr A separate command seems unnecessary; why not just let users set a PYENSEMBL_CACHE_DIRECTORY environment variable?

kippakers commented 9 years ago

Both would work in my opinion. I'd say that permanently setting environmental variables is a step above running a command in difficulty/confusion potential for entry level bioinformatics people.

iskandr commented 9 years ago

Made some progress in this direction with https://github.com/hammerlab/pyensembl/pull/127 and https://github.com/hammerlab/datacache/pull/27, now need to actually expose this to the user.

willgdjones commented 7 years ago

Did this die out? Would be very useful for me.

0xaf1f commented 7 years ago

This issue should probably be closed, since you can apparently set PYENSEMBL_CACHE_DIR to change your cache location. See https://github.com/hammerlab/pyensembl#cache-location