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jmschrei / bpnet-lite

This repository hosts a minimal version of a Python API for BPNet.
MIT License
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TOMTOM missed #2

Closed wang3702 closed 1 year ago

wang3702 commented 1 year ago

I noticed one of your dependency TOMTOM for motif search in this repo https://github.com/jmschrei/bpnet-lite/ is not configured. Then it will raise the following error: sh: tomtom: command not found

Could you please update the dependency configuration to fix it? Thank you!

jmschrei commented 1 year ago

Is this specifically when using the modisco command?

wang3702 commented 1 year ago

Yes. Actually, the dependency is also missing for https://github.com/jmschrei/tfmodisco-lite.

bytewife commented 1 year ago

This is tricky becauses tomtom, and as far as I know, isn't provided through PyPI. But it is provided through conda's bioconda channel. Can be installed with conda install -c bioconda meme. For now we'll update modisco-lite to print that tomtom is missing, and how to install it with the aforementioned command.

wang3702 commented 1 year ago

Thank you! That would be great!