fix: remove deleted azure_batch scripts from Dockerfile

- Remove COPY scripts/azure_batch which no longer exists in the repo
- Remove chmod +x on azure_batch scripts
- Add entrypoint.sh (user/group permission management via gosu)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Author: raylim

Dockerfile

@@ -104,10 +104,6 @@ WORKDIR /app
 # Copy only the installed package from site-packages, not all source files
 RUN mkdir -p /app
 
-# Copy scripts directory for Azure Batch
-COPY scripts /app/scripts
-RUN chmod +x /app/scripts/azure_batch/*.sh
-
 COPY entrypoint.sh /usr/local/bin/entrypoint.sh
 RUN chmod +x /usr/local/bin/entrypoint.sh
 

entrypoint.sh

@@ -0,0 +1,52 @@
+#!/bin/bash
+set -e
+
+# Entrypoint script for Mussel container
+# Manages user permissions and runs commands with proper UID/GID
+
+# Get the user ID and group ID from environment or use defaults
+USER_ID="${MUSSEL_UID:-1000}"
+GROUP_ID="${MUSSEL_GID:-1000}"
+
+# Create a user with the specified UID/GID if running as root and custom UID is requested
+if [ "$(id -u)" = "0" ] && [ "$USER_ID" != "0" ]; then
+  # Create group if it doesn't exist
+  if ! getent group mussel >/dev/null 2>&1; then
+    groupadd -g "$GROUP_ID" mussel
+  fi
+
+  # Create user if it doesn't exist
+  if ! id -u mussel >/dev/null 2>&1; then
+    useradd -u "$USER_ID" -g "$GROUP_ID" -m -s /bin/bash mussel
+  fi
+
+  # Ensure writable cache directories
+  mkdir -p /.cache /tmp
+  chown -R mussel:mussel /.cache /tmp || true
+  chmod -R 777 /.cache /tmp
+
+  # Ensure output directory exists and is writable (Azure Batch expects this)
+  if [ -n "$AZ_BATCH_TASK_WORKING_DIR" ]; then
+    mkdir -p "$AZ_BATCH_TASK_WORKING_DIR/output"
+    chmod -R 777 "$AZ_BATCH_TASK_WORKING_DIR/output" || true
+  fi
+  mkdir -p /tmp/output
+  chmod 777 /tmp/output || true
+  
+  # Ensure cache directories are writable by mussel user if they're set
+  if [ -n "$TMPDIR" ] && [ -d "$TMPDIR" ]; then
+    chown -R mussel:mussel "$TMPDIR" 2>/dev/null || chmod -R 777 "$TMPDIR" 2>/dev/null || true
+  fi
+  if [ -n "$TORCH_HOME" ] && [ -d "$TORCH_HOME" ]; then
+    chown -R mussel:mussel "$TORCH_HOME" 2>/dev/null || chmod -R 777 "$TORCH_HOME" 2>/dev/null || true
+  fi
+  if [ -n "$HF_HOME" ] && [ -d "$HF_HOME" ]; then
+    chown -R mussel:mussel "$HF_HOME" 2>/dev/null || chmod -R 777 "$HF_HOME" 2>/dev/null || true
+  fi
+
+  # Switch to the created user and execute the command
+  exec gosu mussel "$@"
+else
+  # Not root or no custom UID requested - run directly
+  exec "$@"
+fi