knowengdev/jupyterhub_knoweng repository overview

⁠Knowledge Engine for Genomics (KnowEnG) Jupyterhub Server

Dockerfile on GitHub (requires login)⁠

⁠Prerequisite: Install Docker⁠

• Before starting the knoweng_jupyterhub server container check to be sure it is not running. docker ps -a

• if "knoweng_jupyterhub" is on that list you must stop and remove it first. docker stop knoweng_jupyterhub docker rm knoweng_jupyterhub

( Create a directory to run the server so that the files won't clutter up your other directories ) 1 Change to the directory where you will mount the server.

2 Create the container; it will be pulled automatically. docker create -p 8000:8000 --name=knoweng_jupyterhub -v `pwd`:/srv/jupyterhub_mount -i knowengdev/jupyterhub_knoweng:knoweng_jupyterhub_server_with_R_05_25_2018

3 Start the container. docker start knoweng_jupyterhub

4 Start the server. docker exec -w /srv/jupyterhub knoweng_jupyterhub ./simple_start &> jupyterhub.log &

5 Copy this URL http://localhost:8000 into a browser window

• login as "knowengadmin" with password "knowengadmin".
• Use the admin control panel to add or delete users from the jupyterhub server.
• Set user passwords from the host command line. docker exec -i knoweng_jupyterhub passwd username

Server Admin illustrated help⁠

⁠Backup Procedures.

⁠Save the users

1 Run the save users script. docker exec -i knoweng_jupyterhub /scrp/save_users

2 Copy the users data to the mounted directory. docker exec -i knoweng_jupyterhub mv /root/move /srv/jupyterhub_mount/

⁠Restore the users to a NEW container.

docker stop knoweng_jupyterhub docker rm knoweng_jupyterhub

1 Create a container with a new name in the directory were the users are saved ( /move). docker create -p 8000:8000 --name=knoweng_jupyterhub_II -v `pwd`:/srv/jupyterhub_mount -i knowengdev/jupyterhub_knoweng:knoweng_jupyterhub_server_05_04_2018

1. Start the container. docker start knoweng_jupyterhub_II

2 Copy the saved user files into the new container. docker exec -i knoweng_jupyterhub_II mv /srv/jupyterhub_mount/move /root/move_in

• The saved user data will overwrite data in the container if file names are same.

3 Reinstall the saved user files. docker exec -i knoweng_jupyterhub_II /scrp/restore_users

4 Start the server with the newly installed users. docker exec -w /srv/jupyterhub knoweng_jupyterhub_II ./simple_start &> jupyterhub.log &

5 Login as before. http://localhost:8000

• All users EXCEPT knowengadmin, knowengdeveloper, guest and ubuntu_x will retain their old passwords.
• Users may not show up in the control panel until they login.