fail in running the rdkit hparam for lincs

theislab / chemCPA

Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.

https://arxiv.org/abs/2204.13545

MIT License

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fail in running the rdkit hparam for lincs #113

Closed huawen-poppy closed 1 year ago

huawen-poppy commented 1 year ago

Dear developers, thanks for your inspiring tools!

When I tried to run the config_lincs_rdkit_hparam_sweep.yaml file using seml under the experiments/lincs_rdkit_hparam directory, I failed. The error shows like below:

Then I have a check on the config_lincs_rdkit_hparam_sweep.yaml file. I found its executable file is set to chemCPA/seml_sweep_icb.py, which doesn't exist. Could you please guide me to run the process correctly? Thank you very much for your help in advance!

siboehm commented 1 year ago

Yeah you should probably point it: https://github.com/theislab/chemCPA/blob/main/chemCPA/experiments_run.py instead. We must've renamed it.

Be sure to set up seml properly (if you want to use their functionality for tracking the experiments), instructions are in their repo: https://github.com/TUM-DAML/seml

huawen-poppy commented 1 year ago

I see. Thank you for your reply!