# QIIME2

## Disclaimer

Before working with JupyterLab and the Cluster, it is **highly** recommended that you read all the previous articles on the [Cluster](https://guides.tjhsst.edu/research/cluster-introduction), [Slurm](https://guides.tjhsst.edu/research/using-infoprism), and [OnDemand](https://guides.tjhsst.edu/research/ondemand). 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](https://guides.tjhsst.edu/research/ondemand))
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](https://1387849666-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LOujpwpsPzbFQLluKss%2F-MI_LhhqGBnvsJbNBbEi%2F-MI_Q7uMwKe1Rxy5Wbyw%2FScreenshot_20201001_142837.png?alt=media\&token=b9feaea7-eac1-4c4e-b6f1-842d1cc0bb50)

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.