Environment Setup¶

This page covers how to access Alpine during the workshop and set up your working directory. If you have not yet created your account or installed QIIME2, complete the Account & Access page first.

Accessing Alpine During the Workshop¶

Go to ondemand-rmacc.rc.colorado.edu
Log in with your institutional credentials
Go to Clusters → Alpine Shell Access

Requesting an Interactive Compute Node¶

Login nodes are for light tasks only, all QIIME2 commands must run on a compute node. At the start of each workshop day, request an interactive session using the workshop reservation:

sinteractive --reservation=microbiome --ntasks=4 --time=04:00:00

Reservation Availability

The --reservation=microbiome flag is only valid during scheduled workshop hours. Outside of the workshop, omit it:

sinteractive --ntasks=4 --time=04:00:00

Loading QIIME2¶

Once your interactive session starts, load the QIIME2 module:

module purge
module load qiime2/2026.1_amplicon

Verify it loaded correctly:

qiime info

You should see a list of installed plugins. Run these two commands at the start of every workshop session.

Creating Your Working Directory¶

All workshop files will live in a single directory on Alpine scratch storage. Create it once before Day 1:

mkdir /scratch/alpine/YOUR_USERNAME@colostate.edu/qiime2_tutorial
cd /scratch/alpine/YOUR_USERNAME@colostate.edu/qiime2_tutorial

Scratch Storage

Scratch storage on Alpine is not backed up and files may be purged after 90 days of inactivity. Copy important results to /pl/active/ or your local machine when the workshop concludes.

Getting the Workshop Metadata¶

Copy the sample metadata file into your working directory:

cp /pl/active/courses/2025_summer/CSU_2025/q2_workshop_final/QIIME2/metadata_q2_workshop.txt .

After this step your working directory should contain one file:

qiime2_tutorial/ └── metadata_q2_workshop.txt

See the Workshop Data page for a description of the metadata columns.

Next: Workshop Data