From be5c6db5e770fa3fe065f7e28af9ac5cce86a784 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 15 Nov 2024 09:14:54 +0100 Subject: [PATCH 1/3] Update colabfold image to fix running on cpus --- dockerfiles/Dockerfile_nfcore-proteinfold_colabfold | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/dockerfiles/Dockerfile_nfcore-proteinfold_colabfold b/dockerfiles/Dockerfile_nfcore-proteinfold_colabfold index 2ac1f851..6613e061 100644 --- a/dockerfiles/Dockerfile_nfcore-proteinfold_colabfold +++ b/dockerfiles/Dockerfile_nfcore-proteinfold_colabfold @@ -27,7 +27,9 @@ RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \ RUN cd / \ && wget https://raw.githubusercontent.com/YoshitakaMo/localcolabfold/82a3635/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 \ + # Avoid error running on cpus + # https://github.com/YoshitakaMo/localcolabfold/issues/238#issuecomment-2203777538 + && sed -i "/==0.4.28/d" install_colabbatch_linux.sh \ && bash install_colabbatch_linux.sh RUN /localcolabfold/colabfold-conda/bin/python3.10 -m pip install tensorflow-cpu==2.11.0 From 6a7c46e827751dd3c807acd827cb3ba6211ca9fe Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 15 Nov 2024 09:34:10 +0100 Subject: [PATCH 2/3] Update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 25051396..503d8903 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[#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. +- [[#214](https://github.com/nf-core/proteinfold/issues/214)]- Fix colabfold image to run in cpus after [#188](https://github.com/nf-core/proteinfold/issues/188) fix. ## [[1.1.1](https://github.com/nf-core/proteinfold/releases/tag/1.1.1)] - 2025-07-30 From 22f3a2bc1390ed9a7212f641d3fea05fd72dee31 Mon Sep 17 00:00:00 2001 From: Jose Espinosa-Carrasco Date: Fri, 15 Nov 2024 09:44:52 +0000 Subject: [PATCH 3/3] Make lint happy --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 826f6ff6..b947eccd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,7 +16,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[PR #210](https://github.com/nf-core/proteinfold/pull/210)]- Moving post-processing logic to a subworkflow, change wave images pointing to oras to point to https and refactor module to match nf-core folder structure. - [[#214](https://github.com/nf-core/proteinfold/issues/214)]- Fix colabfold image to run in cpus after [#188](https://github.com/nf-core/proteinfold/issues/188) fix. - ## [[1.1.1](https://github.com/nf-core/proteinfold/releases/tag/1.1.1)] - 2025-07-30 ### Enhancements & fixes