1. Request an account for biohpc at  https://biohpc.cornell.edu/lab/lab.aspx

2. Add or remove users from the mongo-db access list

Any user on the access list can add or remove users: 

[root@cbsujohnson ~]# docker1 access list

Container   UserID

infant-mongo-db ad596

infant-mongo-db sw835

infant-mongo-db ap689

[root@cbsujohnson ~]#

To add or remove users, use the command: 

[root@cbsujohnson docker]# docker1 access

docker1 access list

   prints current access list

docker1 access remove <container name> <user id>

   Removes access for <user id> to <container name>

docker1 access add <container name> <user id>

   Adds access for <user id> to <container name>

3. Steps to get access to the data pipeline

a. at your computer terminal, type: ssh yournetid@cbsujohnson.biohpc.cornell.edu

b. enter your password 

(c. type: screen -r)

d. run the following command: 

docker1 run \

  --volume "/workdir/yournetid/get_colors:/home/jovyan/work" \

  -p 8031:8888 \

  --env "GRANT_SUDO=yes" \

  --env "PATH=/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin" \

  --env "DEBIAN_FRONTEND=noninteractive" \

  --env "CONDA_DIR=/opt/conda" \

  --env "SHELL=/bin/bash" \

  --env "NB_USER=jovyan" \

  --env "NB_UID=1000" \

  --env "NB_GID=100" \

  --env "LC_ALL=en_US.UTF-8" \

  --env "LANG=en_US.UTF-8" \

  --env "LANGUAGE=en_US.UTF-8" \

  --env "HOME=/home/jovyan" \

  --env "XDG_CACHE_HOME=/home/jovyan/.cache/" \

  --label "maintainer"="Jupyter Project " \

  --interactive \

  "jupyter/tensorflow-notebook:20221209" \

  "start-notebook.sh"

You will see a token like this:  http://127.0.0.1:8888/lab?token=c7007fb9f1a6aea3c4685328c35741c968d2e24e8821ce2d

Add the highlighted part of the token to: 

http://cbsujohnson.biohpc.cornell.edu:8031/lab?token=XXX

In this case, it would be:

http://cbsujohnson.biohpc.cornell.edu:8031/lab?token=c7007fb9f1a6aea3c4685328c35741c968d2e24e8821ce2d

Copy this link to your browser, you can then see the jupyter notebook page

4. Steps to edit and run the data pipeline in your computer terminal:

(Currently don't have permission to edit or run Jupyter Notebook in Browser, the connection was interrupted) 

a. cd /workdir/yournetid/get_colors

b. vim /local/workdir/yournetid/get_colors/extract_colors_pipeline.py

c. search mode(find where you hope to edit): type \

d. edit mode: type i (insert) 

e. save and quit: esc,  type :(column) wq, then hit enter

f.  to run: type python /local/workdir/yournetid/get_colors/extract_colors_pipeline.py

google doc version of this documentation:  https://docs.google.com/document/d/10mJzJUvUKSlWoK7e-n8yJ-766NdSm0LfIWmDjoRTBQ8/edit