Added mount-farm script.

Added mount-farm.sh script to make it easier for users to mount /nfs /lustre and /warehouse to their instance. The script is copied to /usr/local/bin during post start tasks and can be run just by typing 'mount-farm'.

Dockerfile

@@ -207,8 +207,6 @@ COPY files/notebooks /home/jovyan/notebooks
 
 # copy mount script
 COPY mount-farm.sh /
-RUN sudo chmod +x /mount-farm.sh
-RUN sudo mv /mount-farm.sh /usr/local/bin/mount-farm
 
 # copy poststart script
 COPY poststart.sh /

mount-farm.sh

@@ -0,0 +1,20 @@
+#!/usr/bin/env bash
+
+MOUNTED_DIRS=$(mount | grep sshfs | awk '{print $3}' | grep -E "^(/nfs|/lustre|/warehouse)$")
+if [[ ! -z ${MOUNTED_DIRS} ]];
+then
+   echo "[+] Unmounting previous mounted folders ($(echo $MOUNTED_DIRS | paste -sd "," -))"
+   sudo umount ${MOUNTED_DIRS}
+fi
+
+read -p "[>] Input your farm user: " SANGER_USER
+read -sp "[>] Input your farm password: " SANGER_PASSWORD
+echo ""
+echo "[+] Mounting:"
+for MOUNT_POINT in /nfs /lustre /warehouse; do
+    echo -e "\t- ${MOUNT_POINT}"
+    if [ ! -d "$MOUNT_POINT" ]; then
+        sudo mkdir -p ${MOUNT_POINT}
+    fi
+    echo "${SANGER_PASSWORD}" | sudo sshfs -o password_stdin,allow_other,auto_unmount,no_remote_lock,StrictHostKeyChecking=no ${SANGER_USER}@farm4-login:${MOUNT_POINT} ${MOUNT_POINT}
+done 

poststart.sh

@@ -18,4 +18,7 @@ sudo mkdir -p /nfs
 sudo mkdir -p /lustre
 sudo mkdir -p /warehouse
 
+sudo chmod +x /mount-farm.sh
+sudo cp /mount-farm.sh /usr/local/bin/mount-farm
+
 export USER=jovyan