# 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.