---
# System prepended metadata

title: Installing qiimo on Bridges-2
tags: [Bridges2, Spring 2024, PSC]

---

# Installing `qiime` on Bridges-2

## Setup
:::info
:100: Run the setup steps independently of the method you use to install `qiime`
:::

The first thing you need to do is allocate an interactive session to do your install

```
interact
```

Run these commands on terminal. These commands will create a folder to save your installations

```
DIRECTORY=/ocean/projects/bio240004p/$(whoami)/local

if [ ! -d $DIRECTORY ]; then
    mkdir -p $DIRECTORY
fi

ln -s $DIRECTORY $HOME/.local
```

and

```
DIRECTORY=/ocean/projects/bio240004p/$(whoami)/conda

if [ ! -d $DIRECTORY ]; then
    mkdir -p $DIRECTORY
fi

ln -s $DIRECTORY $HOME/.conda
```

## Using Anaconda
We can use the existing conda distribution to install qiime. To do this run these commands

```
module load anaconda3
wget -nc https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2023.9-py38-linux-conda.yml
conda env create -n qiime2-amplicon-2023.9 --file qiime2-amplicon-2023.9-py38-linux-conda.yml
```

:::warning
The steps above will take a while to run.
:::


## Using Miniconda
Alternatively you can install your own version of Miniconda.

```
wget -nc https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash ./Miniconda3-latest-Linux-x86_64.sh
```

when the software asks where to install, select your project folder. For example, I would choose

```
/ocean/projects/bio240004p/icaoberg
```

if I was part of your project.

After it finishes installing Miniconda follow the instructions on the screen. 

When Miniconda is active then run these commands

```
wget -nc https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2023.9-py38-linux-conda.yml
conda env create -n qiime2-amplicon-2023.9 --file qiime2-amplicon-2023.9-py38-linux-conda.yml
```

to install `qiime` in its own environment.