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kipoi / models

Model zoo for genomics
http://kipoi.org
MIT License
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Added DeepSTARR #290

Closed bernardo-de-almeida closed 2 years ago

bernardo-de-almeida commented 2 years ago

Add the DeepSTARR model for DNA sequence prediction of enhancer activities.

Zenodo: https://doi.org/10.5281/zenodo.5502060 Code: https://github.com/bernardo-de-almeida/DeepSTARR/tree/main/DeepSTARR Manuscript: https://www.biorxiv.org/content/10.1101/2021.10.05.463203

bernardo-de-almeida commented 2 years ago

I have performed the suggested changes, can you test it now? Many thanks

haimasree commented 2 years ago

I have performed the suggested changes, can you test it now? Many thanks

The conda environment does not seem to resolve now (which it did before). It fails at resolving pyrle 0.0.33. I am suspecting this conda environment resolved in your operating system. Which OS is this and which version of pyrle do you have in your environment? The CI is taking place on ubuntu 2021-04

haimasree commented 2 years ago

Any objection on the pinned versions that I suggested? The reason I ask is they were from a successfully resolved conda environment.

bernardo-de-almeida commented 2 years ago

We have CentOS 7.9 and pyrle 0.0.33. Before I added the versions I currently use in my environment, but I updated now for your suggested pinned versions since they were from a successfully resolved conda environment

haimasree commented 2 years ago

We have CentOS 7.9 and pyrle 0.0.33. Before I added the versions I currently use in my environment, but I updated now for your suggested pinned versions since they were from a successfully resolved conda environment

Great! Thanks for your cooperation. The main test is passing now :). The other test is failing due to a bug in kipoi. I am working on a fix as we speak. I will merge this pr afterwards.

And yeah conda dependencies do vary quite a bit between centos and ubuntu in my experience and not always trivial to resolve. Thats why we are providing docker and singularity containers for each model in kipoi now. The containers will be added in a day or two :)

bernardo-de-almeida commented 2 years ago

Great, many thanks for your help!