# HG changeset patch
# User enis
# Date 1754861524 0
# Node ID 3fd12035e6c9f258c8d76aebc87e108a6a0484db
# Parent  7c660a6be0685bbd9f5df61f8f0f95307cdfba17
planemo upload for repository https://github.com/afgane/gcp_batch_netcat commit 4194f0defc4bebd6c95c76b58860c9ae6b9d1899-dirty

diff -r 7c660a6be068 -r 3fd12035e6c9 Dockerfile
--- a/Dockerfile	Thu Jul 24 23:01:40 2025 +0000
+++ b/Dockerfile	Sun Aug 10 21:32:04 2025 +0000
@@ -16,6 +16,7 @@
     tcpdump \
     nmap \
     vim \
+    nfs-common \
     && rm -rf /var/lib/apt/lists/*
 
 RUN pip3 install --break-system-packages google-cloud-batch
@@ -26,4 +27,5 @@
 RUN echo "alias ll='ls -l'" >> /home/galaxy/.bashrc && \
     chown galaxy:galaxy /home/galaxy/.bashrc
 
-USER galaxy
+# Note: Running as root to allow NFS mounting operations
+# USER galaxy
diff -r 7c660a6be068 -r 3fd12035e6c9 gcp_batch_netcat.py
--- a/gcp_batch_netcat.py	Thu Jul 24 23:01:40 2025 +0000
+++ b/gcp_batch_netcat.py	Sun Aug 10 21:32:04 2025 +0000
@@ -81,12 +81,6 @@
     client = batch_v1.BatchServiceClient()
     logger.info("Batch client created successfully")
 
-    # Define the job using the Python client library objects
-    logger.info("Building job specification...")
-    runnable = batch_v1.Runnable()
-    runnable.container = batch_v1.Runnable.Container()
-    runnable.container.image_uri = "afgane/gcp-batch-netcat:0.2.0"
-
     # Create a comprehensive test script
     test_script = f'''#!/bin/bash
 set -e
@@ -94,6 +88,18 @@
 echo "Target: {target_host}:{target_port}"
 echo "Timestamp: $(date)"
 echo "Container hostname: $(hostname)"
+echo "Host VM Image: galaxy-k8s-boot-v2025-08-10"
+echo "Container Image: afgane/gcp-batch-netcat:0.2.0"
+echo ""
+
+# Basic system info
+echo "=== System Information ==="
+echo "OS Release:"
+cat /etc/os-release | head -5 2>/dev/null || echo "OS release info not available"
+echo "Kernel version:"
+uname -r
+echo "Architecture:"
+uname -m
 echo ""
 
 # Basic network info
@@ -128,6 +134,14 @@
 echo "Netcat result: $nc_result"
 echo ""
 
+# NFS client capabilities
+echo "=== NFS Client Information ==="
+echo "NFS client version:"
+/sbin/mount.nfs -V 2>/dev/null || echo "mount.nfs not available"
+echo "RPC services:"
+rpcinfo -p 2>/dev/null || echo "rpcinfo not available"
+echo ""
+
 # Additional connectivity tests
 echo "=== Additional Connectivity Tests ==="
 echo "Testing external connectivity (Google DNS 8.8.8.8:53):"
@@ -139,12 +153,138 @@
 ip route
 echo ""
 
+# NFS Mount Test
+echo "=== NFS Mount Test ==="
+MOUNT_POINT="/tmp/nfs_test_mount"
+echo "Creating mount point: $MOUNT_POINT"
+mkdir -p "$MOUNT_POINT"
+
+echo "Attempting to mount NFS share..."
+echo "Command: mount -t nfs -o vers=3,tcp {target_host}:/ $MOUNT_POINT"
+
+# Try mounting the NFS share
+mount_result=1
+if mount -t nfs -o vers=3,tcp {target_host}:/ "$MOUNT_POINT" 2>&1; then
+    mount_result=0
+    echo "✓ NFS mount successful!"
+
+    echo ""
+    echo "=== NFS Share Contents ==="
+    echo "Long listing of NFS share root:"
+    ls -la "$MOUNT_POINT" 2>/dev/null || echo "Could not list directory contents"
+
+    echo ""
+    echo "Disk usage of NFS share:"
+    df -h "$MOUNT_POINT" 2>/dev/null || echo "Could not get disk usage"
+
+    echo ""
+    echo "Mount information:"
+    mount | grep "$MOUNT_POINT" || echo "Mount info not found"
+
+    # Try to find common Galaxy directories
+    echo ""
+    echo "=== Looking for Galaxy directories ==="
+    for dir in "database" "database/files" "database/objects" "tools" "shed_tools"; do
+        if [ -d "$MOUNT_POINT/$dir" ]; then
+            echo "✓ Found: $dir"
+            ls -la "$MOUNT_POINT/$dir" | head -10
+        else
+            echo "✗ Not found: $dir"
+        fi
+    done
+
+    echo ""
+    echo "Unmounting NFS share..."
+    umount "$MOUNT_POINT" 2>/dev/null && echo "✓ Unmount successful" || echo "✗ Unmount failed"
+else
+    echo "✗ NFS mount failed"
+    echo "Mount error details above"
+
+    # Try alternative mount options
+    echo ""
+    echo "Trying alternative NFS mount options..."
+    echo "Command: mount -t nfs -o vers=4,tcp {target_host}:/ $MOUNT_POINT"
+    if mount -t nfs -o vers=4,tcp {target_host}:/ "$MOUNT_POINT" 2>&1; then
+        mount_result=0
+        echo "✓ NFS v4 mount successful!"
+        ls -la "$MOUNT_POINT" 2>/dev/null || echo "Could not list directory contents"
+        umount "$MOUNT_POINT" 2>/dev/null && echo "✓ Unmount successful" || echo "✗ Unmount failed"
+    else
+        echo "✗ NFS v4 mount also failed"
+    fi
+fi
+
+# CVMFS Mount Test
+echo ""
+echo "=== CVMFS Access Test ==="
+echo "Checking if CVMFS is bind-mounted from host VM..."
+if [ -d "/cvmfs" ]; then
+    echo "✓ /cvmfs directory exists (bind-mounted from host)"
+    ls -la /cvmfs 2>/dev/null || echo "Could not list /cvmfs contents"
+
+    echo ""
+    echo "Checking for Galaxy CVMFS repository..."
+    cvmfs_result=1
+    if [ -d "/cvmfs/data.galaxyproject.org" ]; then
+        cvmfs_result=0
+        echo "✓ Galaxy CVMFS repository accessible!"
+
+        echo ""
+        echo "=== CVMFS Repository Contents ==="
+        echo "Long listing of CVMFS repository root:"
+        ls -la "/cvmfs/data.galaxyproject.org" 2>/dev/null | head -10 || echo "Could not list directory contents"
+
+        echo ""
+        echo "Checking for Galaxy reference data directories:"
+        for dir in "byhand" "location" "tool-data" "genomes"; do
+            if [ -d "/cvmfs/data.galaxyproject.org/$dir" ]; then
+                echo "✓ Found CVMFS directory: $dir"
+                ls "/cvmfs/data.galaxyproject.org/$dir" | head -5 2>/dev/null || echo "Could not list contents"
+            else
+                echo "✗ Not found: $dir"
+            fi
+        done
+
+        echo ""
+        echo "CVMFS mount information from host:"
+        mount | grep cvmfs || echo "CVMFS mount info not visible from container"
+    else
+        echo "✗ Galaxy CVMFS repository not found at /cvmfs/data.galaxyproject.org"
+        echo "This may indicate:"
+        echo "- CVMFS client not running on host VM"
+        echo "- Repository not mounted on host"
+        echo "- Bind mount not properly configured"
+    fi
+else
+    echo "✗ /cvmfs directory not found"
+    echo "This indicates the bind mount from host VM failed"
+    echo "Expected: /cvmfs from host VM bind-mounted into container"
+fi
+
+echo ""
 echo "=== Final Result ==="
-if [ $nc_result -eq 0 ]; then
-    echo "✓ SUCCESS: Connection to NFS server {target_host}:{target_port} successful"
+if [ $nc_result -eq 0 ] && [ $mount_result -eq 0 ]; then
+    echo "✓ SUCCESS: Both network connectivity and NFS mount to {target_host}:{target_port} successful"
+    if [ $cvmfs_result -eq 0 ]; then
+        echo "✓ BONUS: CVMFS repository mount also successful"
+    else
+        echo "ℹ INFO: CVMFS mount failed (may not be available in this image)"
+    fi
     exit 0
+elif [ $nc_result -eq 0 ]; then
+    echo "⚠ PARTIAL SUCCESS: Network connectivity successful but NFS mount failed"
+    echo "Network connection to {target_host}:{target_port} works, but NFS mounting failed."
+    echo "This suggests:"
+    echo "- NFS server is reachable but may not be properly configured"
+    echo "- NFS export permissions may be incorrect"
+    echo "- NFS version mismatch (tried NFSv3 and NFSv4)"
+    echo "- Firewall may allow port 2049 but block other NFS ports (111, 20048)"
+    if [ $cvmfs_result -eq 0 ]; then
+        echo "✓ CVMFS repository mount was successful"
+    fi
+    exit 1
 else
-    echo "✗ FAILED: Connection to NFS server {target_host}:{target_port} failed"
+    echo "✗ FAILED: Network connectivity to NFS server {target_host}:{target_port} failed"
     echo "This suggests a network connectivity issue between GCP Batch and the NFS server."
     echo "Common causes:"
     echo "- Firewall rules blocking NFS traffic (port 2049)"
@@ -155,13 +295,29 @@
     echo "- Ensure NFS service has type LoadBalancer with external IP"
     echo "- Check GCP firewall rules allow traffic from Batch subnet to NFS"
     echo "- Verify the IP address is the LoadBalancer external IP, not ClusterIP"
+    if [ $cvmfs_result -eq 0 ]; then
+        echo ""
+        echo "✓ CVMFS repository mount was successful (good network connectivity to external services)"
+    fi
     exit 1
 fi
 '''
 
+    # Define the job using the Python client library objects
+    logger.info("Building job specification...")
+    runnable = batch_v1.Runnable()
+    runnable.container = batch_v1.Runnable.Container()
+    runnable.container.image_uri = "afgane/gcp-batch-netcat:0.2.0"
+
+    # Bind mount /cvmfs from the host VM (which has CVMFS client) into the container
+    cvmfs_volume = batch_v1.Volume()
+    cvmfs_volume.host_path = "/cvmfs"
+    cvmfs_volume.mount_path = "/cvmfs"
+    runnable.container.volumes = [cvmfs_volume]
+
     runnable.container.entrypoint = "/bin/bash"
     runnable.container.commands = ["-c", test_script]
-    logger.debug(f"Container config: image={runnable.container.image_uri}, entrypoint={runnable.container.entrypoint}")
+    logger.debug(f"Container config: image={runnable.container.image_uri}, with /cvmfs bind mount from custom VM")
 
     task = batch_v1.TaskSpec()
     task.runnables = [runnable]
@@ -186,8 +342,17 @@
     network_policy = batch_v1.AllocationPolicy.NetworkPolicy()
     network_policy.network_interfaces = [network_interface]
 
+    # Instance policy with custom VM image
+    instance_policy = batch_v1.AllocationPolicy.InstancePolicy()
+    instance_policy.machine_type = "e2-medium"  # Specify machine type for custom image
+    instance_policy.boot_disk = batch_v1.AllocationPolicy.Disk()
+    instance_policy.boot_disk.image = f"projects/{project_id}/global/images/galaxy-k8s-boot-v2025-08-10"
+    instance_policy.boot_disk.size_gb = 99
+    logger.debug(f"Using custom VM image: {instance_policy.boot_disk.image}")
+
     allocation_policy = batch_v1.AllocationPolicy()
     allocation_policy.network = network_policy
+    allocation_policy.instances = [instance_policy]
 
     job = batch_v1.Job()
     job.task_groups = [task_group]
diff -r 7c660a6be068 -r 3fd12035e6c9 gcp_batch_netcat.xml
--- a/gcp_batch_netcat.xml	Thu Jul 24 23:01:40 2025 +0000
+++ b/gcp_batch_netcat.xml	Sun Aug 10 21:32:04 2025 +0000
@@ -25,9 +25,28 @@
         <data name="output" format="txt"/>
     </outputs>
     <help><![CDATA[
+    <help><![CDATA[
 **What it does**
 
-This tool submits a job to GCP Batch to test network connectivity between Batch workers and your NFS server. It provides network debugging to help identify connectivity issues in Galaxy deployments on Google Kubernetes Engine (GKE).
+This tool submits a job to GCP Batch to test network connectivity and NFS mounting between Batch workers and your NFS server. It uses a custom Galaxy VM image and provides comprehensive testing including NFS mount operations, CVMFS repository access, and directory listings to help identify connectivity issues in Galaxy deployments on Google Kubernetes Engine (GKE).
+
+**Test Capabilities**
+
+The tool performs comprehensive testing using a container running on the custom `galaxy-k8s-boot-v2025-08-10` VM image:
+- Network connectivity test (netcat to port 2049)
+- NFS mount test with both NFSv3 and NFSv4
+- Directory listing of the NFS share
+- Galaxy-specific directory detection
+- CVMFS repository access test (via bind mount from host VM)
+- Galaxy reference data verification
+- Disk usage and mount information
+
+**Architecture**
+
+The tool uses a hybrid approach:
+- **Host VM**: Custom `galaxy-k8s-boot-v2025-08-10` image with CVMFS client and NFS utilities
+- **Container**: `afgane/gcp-batch-netcat:0.2.0` with network testing tools
+- **Bind Mount**: `/cvmfs` from host VM is bind-mounted into the container for CVMFS access
 
 **Required: NFS LoadBalancer External IP**
 
@@ -39,14 +58,35 @@
 
 To find the correct IP address, run:
 ```
-kubectl get svc -n nfs-provisioner
+kubectl get svc | grep nfs
+kubectl get svc <nfs-service-name> -o wide
 ```
 
 Look for the "EXTERNAL-IP" column for LoadBalancer type services.
 
 **Important: LoadBalancer Configuration**
 
-For NFS connectivity from GCP Batch jobs, your NFS server must be exposed via a LoadBalancer service with an external IP. Internal ClusterIP services are not accessible from external Batch workers.
+For NFS connectivity from GCP Batch jobs, your NFS server must be exposed via a LoadBalancer service with an external IP. The tool also requires:
+- NFS ports (2049, 111, 20048) accessible from external networks
+- Proper NFS export configuration allowing external mounts
+- VM runs with sufficient privileges for mount operations
+
+**Troubleshooting Results**
+
+The tool provides detailed diagnostics:
+- **Network connectivity success + NFS mount success**: Everything working correctly
+- **Network connectivity success + NFS mount failure**: Network works but NFS configuration issues
+- **Network connectivity failure**: Firewall or LoadBalancer configuration issues
+- **CVMFS mount success/failure**: Indicates broader network connectivity and VM image capabilities
+
+**Best Practices**
+
+1. Ensure your NFS service is exposed as type LoadBalancer with an external IP
+2. Verify GCP firewall rules allow traffic from Batch subnet to NFS LoadBalancer IP on ports 2049, 111, and 20048
+3. Check NFS export configuration allows mounting from external IPs
+4. Test the connection manually: `telnet <EXTERNAL-IP> 2049`
+5. Verify the custom VM image is available in your GCP project
+    ]]>
 
     ]]></help>
 </tool>