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kalininalab / alphafold_non_docker

AlphaFold2 non-docker setup
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Add aria2c to conda env #6

Closed aozalevsky closed 2 years ago

aozalevsky commented 2 years ago

As was pointed out in the twitter aria2c is a non-standard package, especially in HPC environments. Adding it in conda env and modifying the manual in a way, such as DB download would already be in the activated conda env might be a nice move.

sanjaysrikakulam commented 2 years ago

Hi @aozalevsky

I will probably create a bash/python script that just uses wget and already existing system tools for downloading and extracting the data and I'll also add relevant documentation. Aria2c seem to require few dependencies and might need IT for that, also the bioconda version of it did not work because it still depends on OpenSSL 1.0.0 libs (not good).

aozalevsky commented 2 years ago

Good solution!

sanjaysrikakulam commented 2 years ago

Hi @aozalevsky

I have added a DB download script to the repo and required documentation to the readme. I did not have the opportunity to test the script completely, but it should work. Along with this, reduced_dbs support is also now available for minimalistic runs.