diff --git a/CHANGELOG.md b/CHANGELOG.md index fa5bc54a..3b38df49 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[PR #178](https://github.com/nf-core/proteinfold/pull/178)] - Enable running multiple modes in parallel. - [[#179](https://github.com/nf-core/proteinfold/issues/179)]- Produce an interactive html report for the predicted structures. - [[#180](https://github.com/nf-core/proteinfold/issues/180)]- Implement Fooldseek. +- [[#188](https://github.com/nf-core/proteinfold/issues/188)]- Fix colabfold image to run in gpus. ## [[1.1.1](https://github.com/nf-core/proteinfold/releases/tag/1.1.1)] - 2025-07-30 diff --git a/dockerfiles/Dockerfile_nfcore-proteinfold_colabfold b/dockerfiles/Dockerfile_nfcore-proteinfold_colabfold index 2ac1f851..cb63d343 100644 --- a/dockerfiles/Dockerfile_nfcore-proteinfold_colabfold +++ b/dockerfiles/Dockerfile_nfcore-proteinfold_colabfold @@ -1,8 +1,8 @@ -FROM nvidia/cuda:11.4.3-cudnn8-runtime-ubuntu18.04 +FROM nvidia/cuda:12.6.2-cudnn-runtime-ubuntu24.04 LABEL authors="Athanasios Baltzis, Jose Espinosa-Carrasco, Leila Mansouri" \ title="nfcore/proteinfold_colabfold" \ - Version="1.1.0" \ + Version="1.2.0dev" \ description="Docker image containing all software requirements to run the COLABFOLD_BATCH module using the nf-core/proteinfold pipeline" ENV PATH="/localcolabfold/colabfold-conda/bin:$PATH" @@ -14,7 +14,7 @@ ENV PATH="/MMseqs2/build/bin:$PATH" RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys A4B469963BF863CC RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \ build-essential \ - cuda-command-line-tools-11-4 \ + cuda-command-line-tools-12-6 \ git \ hmmer \ kalign \ @@ -25,13 +25,13 @@ RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \ && rm -rf /var/lib/apt/lists/* RUN cd / \ - && wget https://raw.githubusercontent.com/YoshitakaMo/localcolabfold/82a3635/install_colabbatch_linux.sh \ + && wget https://raw.githubusercontent.com/YoshitakaMo/localcolabfold/07e87ed/install_colabbatch_linux.sh \ && sed -i "/colabfold.download/d" install_colabbatch_linux.sh \ - && sed -i "s|cudatoolkit==.*\sopenmm|cudatoolkit==11.1.1 openmm|g" install_colabbatch_linux.sh \ && bash install_colabbatch_linux.sh -RUN /localcolabfold/colabfold-conda/bin/python3.10 -m pip install tensorflow-cpu==2.11.0 +## Updated +RUN /localcolabfold/colabfold-conda/bin/python3.10 -m pip install tensorflow-cpu==2.17.0 -#Silence download of the AlphaFold2 params +# #Silence download of the AlphaFold2 params RUN sed -i "s|download_alphafold_params(|#download_alphafold_params(|g" /localcolabfold/colabfold-conda/lib/python3.10/site-packages/colabfold/batch.py RUN sed -i "s|if args\.num_models|#if args\.num_models|g" /localcolabfold/colabfold-conda/lib/python3.10/site-packages/colabfold/batch.py