> For the complete documentation index, see [llms.txt](https://guides.tjhsst.edu/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://guides.tjhsst.edu/research/ondemand/qiime2.md).

# QIIME2

## Disclaimer

Before working with JupyterLab and the Cluster, it is **highly** recommended that you read all the previous articles on the [Cluster](/research/cluster-introduction.md), [Slurm](/research/using-infoprism.md), and [OnDemand](/research/ondemand.md). Running into the Cluster without knowing how the various features work will not be an enjoyable experience for you.

## Running Qiime2

### Logging in 

1. Create a JupyterLab session on OnDemand (see [OnDemand](/research/ondemand.md))
2. You will be placed into a queue until a computer is allocated to you (one of 40+ machines)
3. 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.

### Activating qiime2

`qiime2` and related packages are installed in the `qiime2` module. This environment can also be accessed through JupyterLab with the "Console" and "Notebook" options (Python only). To access `qiime2` from the terminal run the following:

```bash
module load qiime2
```

Now you can run `qiime` to access Qiime2

### Qiime2 Through Jupyter

After accessing Jupyter, you should see the following on the "launcher":

![Notice the Qiime2 options in Notebook and Console. Also notice the R(qiime2) options](/files/-MI_Q7uMwKe1Rxy5Wbyw)

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.