QIIME2
This document describes how to use qiime2 and other biology packages on JupyterHub and the Cluster
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This document describes how to use qiime2 and other biology packages on JupyterHub and the Cluster
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Before working with JupyterHub and the Cluster it is highly recommended that you read all the previous articles on the , , , and , (official conda docs ). Running into the Cluster without knowing how the various features work will not be an enjoyable experience for you.
Log into 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:
The terminal prompt should now look something like this (noticed the (qiime2)
preceding):
Now you can run qiime
to access Qiime2
After logging into JupyterHub you should see the following on the JupyterHub "launcher":
The 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.