update dev container setup

.devcontainer/Dockerfile

@@ -4,23 +4,68 @@ FROM golang:1.21 AS golang
 #========================================================================================================#
 FROM xenonmiddleware/slurm:20
 
+#==============================================================================================
+# Define ARGs
+ARG HADDOCK_VERSION=v3.0.0-beta.5
 ARG USERNAME=dev
 ARG USER_UID=1000
 ARG USER_GID=$USER_UID
 
+#==============================================================================================
+# Install system dependencies
+RUN apt-get update \
+  && apt-get install -y --no-install-recommends \
+  build-essential=12.1ubuntu2 \
+  sudo=1.8.16-0ubuntu1.10 \
+  wget=1.17.1-1ubuntu1.5 \
+  git=1:2.7.4-0ubuntu1.10 \
+  && apt-get clean \
+  && rm -rf /var/lib/apt/lists/*
+
+#==============================================================================================
+# Configure User
 RUN groupadd --gid $USER_GID $USERNAME \
   && useradd --uid $USER_UID --gid $USER_GID -m $USERNAME \
-  && apt-get update \
-  && apt-get install -y --no-install-recommends sudo=1.8.16-0ubuntu1.10 \
-  && apt-get clean \
-  && rm -rf /var/lib/apt/lists/* \
   && echo $USERNAME ALL=\(root\) NOPASSWD:ALL > /etc/sudoers.d/$USERNAME \
   && chmod 0440 /etc/sudoers.d/$USERNAME
 
+#==============================================================================================
+# Install miniconda
+ENV CONDA_DIR /opt/conda
+RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh  \
+  && /bin/bash ~/miniconda.sh -b -p /opt/conda
+
+ENV PATH=$CONDA_DIR/bin:$PATH
+RUN conda install python=3.9
+
+#==============================================================================================
+# Install HADDOCK3
+WORKDIR /opt
+
+RUN git clone --recursive https://github.com/haddocking/haddock3.git
+WORKDIR /opt/haddock3
+RUN git checkout ${HADDOCK_VERSION}
+
+WORKDIR /opt/haddock3/src/fcc/src
+RUN make
+
+WORKDIR /opt/haddock3
+RUN pip install --no-cache-dir -r requirements.txt \
+  && python setup.py develop
+
+WORKDIR /opt/haddock3/bin
+COPY cns /opt/haddock3/bin/cns
+
+#==============================================================================================
+# Copy Go
+COPY --from=golang /usr/local/go/ /usr/local/go/
+
+#========================================================================================================#
+# Configure container startup
 WORKDIR /app
 COPY start.sh /app/start.sh
 RUN chmod +x /app/start.sh
 
-COPY --from=golang /usr/local/go/ /usr/local/go/
-
+USER $USERNAME
+WORKDIR $HOME
 #========================================================================================================#

.devcontainer/devcontainer.json

@@ -1,16 +1,24 @@
 {
   "build": {
-    "dockerfile": "Dockerfile"
+    "dockerfile": "Dockerfile",
   },
   "features": {
     "ghcr.io/devcontainers/features/go:1": {},
-    "ghcr.io/devcontainers/features/git:1": {}
+    "ghcr.io/devcontainers/features/git:1": {},
   },
-  "postCreateCommand": "sudo /app/start.sh",
+  "postCreateCommand": "sudo bash /app/start.sh",
   "customizations": {
     "vscode": {
-      "extensions": ["golang.go", "GitHub.copilot"]
-    }
+      "extensions": ["golang.go", "GitHub.copilot"],
+      "settings": {
+        "terminal.integrated.defaultProfile.linux": "bash",
+        "terminal.integrated.profiles.linux": {
+          "zsh": {
+            "path": "/bin/bash",
+          },
+        },
+      },
+    },
   },
-  "containerUser": "dev"
+  "containerUser": "dev",
 }

.gitignore

@@ -2,7 +2,7 @@
 #***********************************************************************
 # VSCode things
 .vscode
-
+.devcontainer/cns
 
 #***********************************************************************
 # Benchmark things

example/example_haddock30.yml

@@ -1,11 +1,12 @@
 general:
-  executable: /home/rodrigo/repos/haddock-runner/example/haddock3.sh
-  max_concurrent: 4
-  haddock_dir: /home/rodrigo/repos/haddock3
+  executable: /workspaces/haddock-runner/example/haddock3.sh
+  max_concurrent: 1
+  haddock_dir: /opt/haddock3
   receptor_suffix: _r_u
   ligand_suffix: _l_u
-  input_list: /home/rodrigo/repos/haddock-runner/example/input_list.txt
-  work_dir: /home/rodrigo/repos/haddock-runner/bm-goes-here
+  input_list: /workspaces/haddock-runner/example/input_list.txt
+  work_dir: /workspaces/haddock-runner/bm-goes-here
+  use_slurm: true
 
 scenarios:
   - name: true-interface
@@ -31,7 +32,7 @@ scenarios:
           unambig_fname: _unambig.tbl
           ligand_top_fname: _ligand.top
           ligand_param_fname: _ligand.param
-        emref:
+        emref: ~
         caprieval:
           reference_fname: _ref.pdb
 

example/haddock3.sh

@@ -1,12 +1,8 @@
 #!/bin/bash
 #===============================================================================
-HADDOCK3_DIR="$HOME/repos/haddock3"
 
-### Activate the virtual environment
-## if your haddock3 installation uses venv
-source "$HADDOCK3_DIR/venv/bin/activate" || exit
-## if your haddock3  installation uses conda
-# conda activate haddock3
+source /opt/conda/etc/profile.d/conda.sh
+conda activate env
 
 haddock3 "$@"
 #===============================================================================