jscgh
There's a pull request to fix this. https://github.com/PaddlePaddle/PaddleHelix/pull/283 In the mean time you can use ```export SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=True```
Thank you, @ppenev-eligo. This issue was resolved as part of the changes merged in https://github.com/nf-core/proteinfold/pull/314
The [version available on our branch](https://github.com/Australian-Structural-Biology-Computing/proteinfold/tree/add-chai) is working but writing out the rest of the boilerplate files is not currently a priority. If anyone is interested in taking over I...
I have updated the dockerfile for the Chai-1 image for a ~25% reduction in size. [It is available on our fork here](https://github.com/Australian-Structural-Biology-Computing/proteinfold/blob/869343cdfc483ad08fec8747ff74e86ad2e5a5de/dockerfiles/Dockerfile_nfcore-proteinfold_chai1). This won't change functionality at all and should...
[I've added](https://github.com/Australian-Structural-Biology-Computing/proteinfold/tree/056ba4f4b6f4a36d4e7fe98407631ee9b582b7fc) `prepare_chai1_dbs.nf`; however, it's not able to download the models yet. It needs to iterate over `components = ["feature_embedding", "token_embedder", "trunk", "diffusion_module", "confidence_head"]` to download `chai1_models_link"/${component}.pt"` I wasn't able...
I have encountered the same error with another protein. ``` { "entities": [ { "type": "protein", "sequence": "MKFQHTFIALLSLLTYANAYDYFTTTLANQNPVCASVDVIQNVCTEVCGRFVRYIPDATNTNQFTFAEYTTNQCTVQVTPAVTNTFTCADQTSSHALGSDWSGVCKITATPAPTVTPTVTPTVTPTVTPTPTNTPNPTPSQTSTTTGSASTVVASLSLIIFSMILSLC", "count": 1 } ] } ``` ``` 2024-10-01 16:59:22 DEBUG Reading PDB...
There's a pull request to fix this. https://github.com/PaddlePaddle/PaddleHelix/pull/283 In the mean time you can use `export SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=True`
Added RP6000 (CUDA Compute Capability 12.0) tests. No current images are compatible.
I am working on this during the hackathon on this [branch](https://github.com/Australian-Structural-Biology-Computing/proteinfold/tree/simplify-helixfold3). - [x] Moved parameters to modules.config - [x] Set ENVs in `Dockerfile` rather than `script:` portion of `main.nf` -...
@JoseEspinosa I was able to run on H200s using the latest `dev` images in the repository. - https://quay.io/repository/nf-core/proteinfold_alphafold2_msa - https://quay.io/repository/nf-core/proteinfold_alphafold2_split Your updated [Dockerfiles](https://github.com/JoseEspinosa/nf-core-proteinfold/tree/update_af2_split_images/dockerfiles) seem to have fixed it. Thank you!