Before working with JupyterHub and the Cluster it is highly recommended that you read all the previous articles on the Cluster, Slurm, JupyterHub, and Conda, (official conda docs here). Running into the Cluster without knowing how the various features work will not be an enjoyable experience for you.
Log into https://jupyterhub.tjhsst.edu through Ion
You will be placed into a queue until a computer is allocated to you (one of 40+ machines)
Once logged in select "File > New > Terminal" this will give you a terminal on the machine you are n
This is the same effect as Running
ssh [Ion username]@remote.tjhsst.edu and then
ssh [computer] from there.
Conda is a package manager that has been installed on these servers. It creates environments in which you can run and install software. You need to initialize conda once for your user account before you can access the qiime2 installation.
If you have never run
conda before run:
/opt/conda/bin/conda init bash && source ~/.bashrc
qiime2 and related packages are installed in the
qiime2 conda environment. This environment can also be accessed through JupyterHub with the "Console" and "Notebook" options (Python only). To access
qiime2 from the terminal run the following:
conda activate qiime2
The terminal prompt should now look something like this (noticed the
(qiime2) borg40 2021abagali $
Now you can run
qiime to access Qiime2
After logging into JupyterHub you should see the following on the JupyterHub "launcher":
qiime2 options will spawn a Python Notebook or Console depending on what you choose. The
R(qiime2) will spawn an R Notebook or Console depending on what you choose.