Updated AF2 standard Dockerfile

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -9,6 +9,7 @@ body:
 
         - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
         - [nf-core/proteinfold pipeline documentation](https://nf-co.re/proteinfold/usage)
+
   - type: textarea
     id: description
     attributes:

.github/workflows/branch.yml

@@ -1,17 +1,15 @@
 name: nf-core branch protection
-# This workflow is triggered on PRs to `main`/`master` branch on the repository
-# It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev`
+# This workflow is triggered on PRs to master branch on the repository
+# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
 on:
   pull_request_target:
-    branches:
-      - main
-      - master
+    branches: [master]
 
 jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      # PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
+      # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
         if: github.repository == 'nf-core/proteinfold'
         run: |
@@ -24,7 +22,7 @@ jobs:
         uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         with:
           message: |
-            ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:
+            ## This PR is against the `master` branch :x:
 
             * Do not close this PR
             * Click _Edit_ and change the `base` to `dev`
@@ -34,9 +32,9 @@ jobs:
 
             Hi @${{ github.event.pull_request.user.login }},
 
-            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) ${{github.event.pull_request.base.ref}} branch.
-            The ${{github.event.pull_request.base.ref}} branch on nf-core repositories should always contain code from the latest release.
-            Because of this, PRs to ${{github.event.pull_request.base.ref}} are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
+            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
+            The `master` branch on nf-core repositories should always contain code from the latest release.
+            Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
 
             You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
             Note that even after this, the test will continue to show as failing until you push a new commit.

.github/workflows/linting_comment.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@80620a5d27ce0ae443b965134db88467fc607b43 # v7
+        uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6
         with:
           workflow: linting.yml
           workflow_conclusion: completed

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v3.1.0"
+    rev: "v4.0.0-alpha.8"
     hooks:
       - id: prettier
         additional_dependencies:

CHANGELOG.md

@@ -10,12 +10,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#177](https://github.com/nf-core/proteinfold/issues/177)] - Fix typo in some instances of model preset `alphafold2_ptm`.
 - [[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.
+- [[#180](https://github.com/nf-core/proteinfold/issues/180)] - Implement Foldseek.
 - [[#188](https://github.com/nf-core/proteinfold/issues/188)] - Fix colabfold image to run in gpus.
 - [[PR ##205](https://github.com/nf-core/proteinfold/pull/205)] - Change input schema from `sequence,fasta` to `id,fasta`.
 - [[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.
 - [[#235](https://github.com/nf-core/proteinfold/issues/235)] - Update samplesheet to new version (switch from `sequence` column to `id`).
+- [[#239](https://github.com/nf-core/proteinfold/issues/239)] - Update alphafold2 standard mode Dockerfile.
 
 ## [[1.1.1](https://github.com/nf-core/proteinfold/releases/tag/1.1.1)] - 2025-07-30
 

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) The nf-core/proteinfold team
+Copyright (c) Athanasios Baltzis, Jose Espinosa-Carrasco, Harshil Patel
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

dockerfiles/Dockerfile_nfcore-proteinfold_alphafold2_standard

@@ -1,22 +1,26 @@
-FROM nvidia/cuda:11.4.3-cudnn8-runtime-ubuntu18.04
+ARG CUDA=12.2.2
+FROM nvidia/cuda:${CUDA}-cudnn8-runtime-ubuntu20.04
+# FROM directive resets ARGS, so we specify again (the value is retained if
+# previously set).
+ARG CUDA
 
 LABEL authors="Athanasios Baltzis, Jose Espinosa-Carrasco, Leila Mansouri" \
     title="nfcore/proteinfold_alphafold2_standard" \
-    Version="1.1.0" \
+    Version="dev" \
     description="Docker image containing all software requirements to run the RUN_ALPHAFOLD2 module using the nf-core/proteinfold pipeline"
 
 # Use bash to support string substitution.
 SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
 # Add env variables
-ENV LD_LIBRARY_PATH="/conda/lib:/usr/local/cuda-11.4/lib64:$LD_LIBRARY_PATH"
-ENV PATH="/conda/bin:$PATH"
+ENV LD_LIBRARY_PATH="/usr/local/cuda-12.2/lib64:$LD_LIBRARY_PATH"
 
 RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys A4B469963BF863CC
-RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y \
+RUN apt-get update --quiet \
+    && DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y --quiet \
     build-essential \
     cmake \
-    cuda-command-line-tools-11-4 \
+    cuda-command-line-tools-$(cut -f1,2 -d- <<< ${CUDA//./-}) \
     git \
     hmmer \
     kalign \
@@ -33,27 +37,26 @@ RUN git clone https://github.com/deepmind/alphafold.git /app/alphafold && \
     cd -
 
 # Compile HHsuite from source
-RUN git clone --branch v3.3.0 https://github.com/soedinglab/hh-suite.git /tmp/hh-suite \
+RUN git clone --branch v3.3.0 --single-branch https://github.com/soedinglab/hh-suite.git /tmp/hh-suite \
     && mkdir /tmp/hh-suite/build \
-    &&  cd /tmp/hh-suite/build \
-    &&  cmake -DCMAKE_INSTALL_PREFIX=/opt/hhsuite -DHAVE_AVX2=1 .. \
+    && cd /tmp/hh-suite/build \
+    && cmake -DCMAKE_INSTALL_PREFIX=/opt/hhsuite .. \
     && make -j 4 && make install \
     && ln -s /opt/hhsuite/bin/* /usr/bin \
     && cd - && rm -rf /tmp/hh-suite
 
-# Install Miniconda package manager
+# Install Miniforge package manager
 RUN wget -q -P /tmp \
-    https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
-    && bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /conda \
-    && rm /tmp/Miniconda3-latest-Linux-x86_64.sh
+    "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" \
+    && bash /tmp/Miniforge3-$(uname)-$(uname -m).sh -b -p /opt/conda \
+    && rm /tmp/Miniforge3-$(uname)-$(uname -m).sh
 
-# Install conda packages
-RUN /conda/bin/conda install -y -c conda-forge \
-    openmm=7.7.0 \
-    cudatoolkit==11.1.1 \
-    pdbfixer \
-    pip \
-    python=3.10 \
+# Install Conda packages.
+ENV PATH="/opt/conda/bin:$PATH"
+ENV LD_LIBRARY_PATH="/opt/conda/lib:$LD_LIBRARY_PATH"
+RUN conda install --quiet --yes conda==24.11.1 pip python=3.11 \
+    && conda install --quiet --yes --channel nvidia cuda=${CUDA_VERSION} \
+    && conda install --quiet --yes --channel conda-forge openmm=8.0.0 pdbfixer \
     && conda clean --all --force-pkgs-dirs --yes
 
 RUN wget -q -P /app/alphafold/alphafold/common/ \
@@ -63,17 +66,26 @@ RUN wget -q -P /app/alphafold/alphafold/common/ \
 RUN pip3 install --upgrade pip --no-cache-dir \
     && pip3 install -r /app/alphafold/requirements.txt --no-cache-dir \
     && pip3 install --upgrade --no-cache-dir \
-    jax==0.3.25 \
-    jaxlib==0.3.25+cuda11.cudnn805 \
+    jax==0.4.26 \
+    jaxlib==0.4.26+cuda12.cudnn89 \
     -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
 
 RUN sed -i "s|alphafold/common/stereo_chemical_props.txt|/app/alphafold/alphafold/common/stereo_chemical_props.txt|g" /app/alphafold/alphafold/common/residue_constants.py
 
 # Add SETUID bit to the ldconfig binary so that non-root users can run it.
 RUN chmod u+s /sbin/ldconfig.real
 
+# Currently needed to avoid undefined_symbol error.
+RUN ln -sf /usr/lib/x86_64-linux-gnu/libffi.so.7 /opt/conda/lib/libffi.so.7
+
 # We need to run `ldconfig` first to ensure GPUs are visible, due to some quirk
 # with Debian. See https://github.com/NVIDIA/nvidia-docker/issues/1399 for
 # details.
-RUN cd /app/alphafold
-RUN ldconfig
+# ENTRYPOINT does not support easily running multiple commands, so instead we
+# write a shell script to wrap them up.
+WORKDIR /app/alphafold
+RUN echo $'#!/bin/bash\n\
+ldconfig\n\
+python /app/alphafold/run_alphafold.py "$@"' > /app/run_alphafold.sh \
+    && chmod +x /app/run_alphafold.sh
+ENTRYPOINT ["/app/run_alphafold.sh"]