From e626c368408922703a47dd8325e3a8075340a7aa Mon Sep 17 00:00:00 2001
From: Tyson Swetnam <tswetnam@cyverse.org>
Date: Fri, 31 Jan 2025 13:07:11 -0700
Subject: [PATCH] created 4.96.4

---
 4.96.4/Dockerfile | 70 +++++++++++++++++++++++++++++++++++++++++++++++
 4.96.4/entry.sh   | 27 ++++++++++++++++++
 2 files changed, 97 insertions(+)
 create mode 100644 4.96.4/Dockerfile
 create mode 100644 4.96.4/entry.sh

diff --git a/4.96.4/Dockerfile b/4.96.4/Dockerfile
new file mode 100644
index 0000000..88b0844
--- /dev/null
+++ b/4.96.4/Dockerfile
@@ -0,0 +1,70 @@
+FROM lscr.io/linuxserver/code-server:4.96.4
+
+USER root
+
+# Install a few dependencies for goCommands, text editing, and monitoring instances
+RUN apt update && \
+    apt install -y lsb-release apt-transport-https curl libfreetype6-dev pkg-config libx11-dev gcc gettext gnupg less software-properties-common apt-utils glances htop nano wget
+
+# Install GoCommands https://learning.cyverse.org/ds/gocommands/ 
+RUN cd /usr/local/bin/ && \
+    GOCMD_VER=$(curl -L -s https://raw.githubusercontent.com/cyverse/gocommands/main/VERSION.txt); \
+    curl -L -s https://github.com/cyverse/gocommands/releases/download/${GOCMD_VER}/gocmd-${GOCMD_VER}-linux-amd64.tar.gz | tar zxvf -
+
+# Add sudo 
+RUN apt update && \
+    apt install -y sudo && \
+    apt clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# Create user vscode with specific UID and GID
+RUN groupadd -g 1000 vscode && \
+    useradd -m -u 1000 -g 1000 -s /bin/bash vscode && \
+    usermod -aG sudo vscode && \
+    echo "vscode ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
+
+# Install cuda toolkit and nvidia drivers
+RUN wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64/cuda-keyring_1.1-1_all.deb && \
+    dpkg -i cuda-keyring_1.1-1_all.deb && \
+    apt update && \
+    apt install -y cuda-toolkit-12-5 nvidia-driver-535 -y
+
+# Set ownership for home directory
+RUN chown -R vscode:vscode /home/vscode && \
+    chown -R vscode:vscode /config
+
+# Install Miniconda and Mamba
+RUN curl -sSLo /tmp/Miniconda3.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
+    bash /tmp/Miniconda3.sh -b -p /opt/conda && \
+    rm /tmp/Miniconda3.sh && \
+    /opt/conda/bin/conda install -y mamba -n base -c conda-forge && \
+    /opt/conda/bin/conda clean -afy && \
+    chown -R vscode:vscode /opt/conda
+
+# Install Ollama and dependecies
+RUN apt install pciutils -y && \
+curl https://ollama.ai/install.sh | sh
+
+#RUN ollama serve & sleep 5 && ollama run mxbai-embed-large
+
+USER vscode
+
+# install git credential manager
+RUN cd /home/vscode && \
+    wget https://github.com/git-ecosystem/git-credential-manager/releases/download/v2.5.0/gcm-linux_amd64.2.5.0.deb && \
+    sudo dpkg -i gcm-linux_amd64.2.5.0.deb && \
+    rm gcm-linux_amd64.2.5.0.deb
+
+# set the ENV for the credential type
+ENV GCM_CREDENTIAL_STORE=cache
+
+EXPOSE 8443
+
+COPY entry.sh /bin
+
+# Set up environment variables for Conda
+ENV PATH="/opt/conda/bin:$PATH"
+
+WORKDIR /home/vscode
+
+ENTRYPOINT ["bash", "/bin/entry.sh"]
diff --git a/4.96.4/entry.sh b/4.96.4/entry.sh
new file mode 100644
index 0000000..db7dacc
--- /dev/null
+++ b/4.96.4/entry.sh
@@ -0,0 +1,27 @@
+#!/bin/bash
+
+# Ensure .irods directory and environment file exist
+mkdir -p /home/vscode/.irods
+cat <<EOF > /home/vscode/.irods/irods_environment.json
+{
+  "irods_host": "data.cyverse.org",
+  "irods_port": 1247,
+  "irods_user_name": "$IPLANT_USER",
+  "irods_zone_name": "iplant"
+}
+EOF
+
+# Add conda to PATH
+# echo "export PATH=$PATH:/opt/conda/bin" >> /home/vscode/.bashrc
+
+# Copy user configurations if they exist
+if [ -f /data-store/iplant/home/$IPLANT_USER/.gitconfig ]; then
+  cp /data-store/iplant/home/$IPLANT_USER/.gitconfig ~/ 
+fi
+
+if [ -d /data-store/iplant/home/$IPLANT_USER/.ssh ]; then
+  cp -r /data-store/iplant/home/$IPLANT_USER/.ssh ~/ 
+fi
+
+# Start code-server
+exec /app/code-server/bin/code-server --host 0.0.0.0 --disable-telemetry --