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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
374 stars 65 forks source link

Remove auto-downloading? #101

Closed tavinathanson closed 9 years ago

tavinathanson commented 9 years ago

Seems like it might be an unnecessary headache, per a conversation with @iskandr. We might just want to require users to manually install via pyensembl install or within Python.

hammer commented 9 years ago

:+1: Please call it download not install though.

tavinathanson commented 9 years ago

@hammer there's currently pyensembl install, pyensembl index and pyensembl download

download: downloads GTF/FASTA files from a server (or, if they're local, just copies them from the local location). index: creates a DB for GTF data and indexes FASTA files. install: download + index

@iskandr and I have been hoping for better names, here. Thoughts?

hammer commented 9 years ago

download and index seem fine; how about download_and_index?

tavinathanson commented 9 years ago

Seems like a long name for something that's going to be (I assume) the most common command.

hammer commented 9 years ago

so give it a shortcut name like dli or something?

tavinathanson commented 9 years ago

While I don't love install, it seems easier to remember than dli or download_and_index. Curious what connotations you think install has that make it inappropriate?

tavinathanson commented 9 years ago

Naming discussion moved to https://github.com/hammerlab/pyensembl/issues/102

tavinathanson commented 9 years ago

Auto-downloading removed in #114