From 53fd4d7e186aa2b330262ad92e2b72f2fcfa8749 Mon Sep 17 00:00:00 2001
From: Geert van Geest <geert.vangeest@bioinformatics.unibe.ch>
Date: Thu, 9 Jan 2025 13:47:09 +0100
Subject: [PATCH] makes additional ports optional

---
 run_jupyter_notebooks | 20 ++++++++++++++++----
 1 file changed, 16 insertions(+), 4 deletions(-)

diff --git a/run_jupyter_notebooks b/run_jupyter_notebooks
index c636d86..66055b4 100755
--- a/run_jupyter_notebooks
+++ b/run_jupyter_notebooks
@@ -10,9 +10,10 @@ This command generates docker containers based on a jupyter notebook container f
 -m maximum memory for the user container. Default: 16g.\n
 -c maximum number of cpu for the user container. Default: 4.\n
 -n container name prefix. Default: jupyter \n
--a add admin container[yes/no]. Default: yes"
+-a add admin container[yes/no]. Default: yes \n
+-d add an additional port at port-2000 [yes/no]. Default: no"
 
-while getopts ":i:u:p:m:c:n:a:" opt
+while getopts ":i:u:p:m:c:n:a:d:" opt
 do
   case $opt in
     i)
@@ -36,6 +37,9 @@ do
     a)
       ADD_ADMIN=$OPTARG
       ;;
+    d)
+      ADD_PORT=$OPTARG
+      ;;
     \?)
       echo -e "Invalid option: -$OPTARG \n" >&2
       echo -e $USAGE >&2
@@ -67,6 +71,7 @@ if [ "$MEMORY" == "" ]; then MEMORY=16g; fi
 if [ "$CPU" == "" ]; then CPU=4; fi
 if [ "$CONTAINER_NAME" == "" ]; then CONTAINER_NAME=jupyter; fi
 if [ "$ADD_ADMIN" == "" ]; then ADD_ADMIN=yes; fi
+if [ "$ADD_PORT" == "" ]; then ADD_PORT=no; fi
 
 # create general volume that will be populated with read-only data
 docker volume create data
@@ -113,6 +118,13 @@ do
   # generate container for each user
   # mount user volume, data volume (general, read only) and group work volume (general, read and write)
   # the permissions of general volumes (data and group work) need to be changed with the master container (this can probably be coded as well)
+  if [ "$ADD_PORT" == "yes" ]
+  then 
+        ADD_PORT="-p $((port-2000)):$((port-2000))"
+  else
+        ADD_PORT=""
+  fi 
+
   docker run \
   -d \
   --cpus=$CPU \
@@ -128,7 +140,7 @@ do
   -e JUPYTER_ENABLE_LAB=yes \
   -e JUPYTER_TOKEN=$password \
   -p $port:8888 \
-  -p $((port-2000)):$((port-2000)) \
+  "$ADD_PORT" \
   $IMAGE \
   start-notebook.sh
 done
@@ -143,4 +155,4 @@ done
 
 # to add https:
 # --ServerApp.keyfile=/etc/ssl/notebook/notebook.key \
-# --ServerApp.certfile=/etc/ssl/notebook/notebook.pem
+# --ServerApp.certfile=/etc/ssl/notebook/notebook.pem
\ No newline at end of file