1 Borah

You can get a Borah account by contacting the Boise State University HPC Team. When asking for a Borah account, you will need to provide the following information:

  • Request Account on the HPC SYSTEM: system name
  • Project: Project Name or Grant Information
  • Description of Research: Short description of research to be done on the cluster.
  • Project PI Name: PI’s-Name.
  • Email Address of Requestor:

Make sure that you let them know you need access to the BioCompute node, which is a node that is dedicated entirely to biology. This will ensure that your jobs get priority.

2 Using SBATCH files on Borah

Many high performance computing (HPC) platforms use a queuing system to ensure computing jobs can get done by multiple users in an easy and equitable way. Jobs on Borah (Boise State University) and Teton (University of Wyoming) are submitted using SBATCH files, which are written in the ‘slurm’ coding language.

These files begin with a list of commands that give details about the job:

#!/bin/bash
#SBATCH -J MPI_TEST # job name
#SBATCH -o log_slurm.o%j # output and error file name (%j expands to jobID)
#SBATCH -n 28 # total number of tasks requested
#SBATCH -N 1 # number of nodes you want to run on
#SBATCH -p defq # queue (partition)
#SBATCH -t 12:00:00 # run time (hh:mm:ss) - 12.0 hours in this example.
#SBATCH --mail-type=END # mail you when your job is complete
#SBATCH --mail-type=BEGIN # mail you when your job has begun
#SBATCH --mail-type=FAIL # mail you when your job has failed
#SBATCH --mail-user=user@domain.edu # email you can be sent notifications to.

This will be followed with any commands that are needed for your job.

3 Access to the Biocompute CIFS-Share

When you contact the HPC Team to create a Borah account, you can also ask them to add your credentials to the BSU Biocompute CIFS-Share. To access the CIFS-Share on a Mac, you can use the following:

4 How do download Anaconda and QIIME2 to your Borah account:

Anaconda is a program that helps with the installation of hundreds of genetic software for Linux.

First, we need to ssh (secure shell) to get onto Borah:

ssh -XC username@borah-login.boisestate.edu
# Enter your password, then you're on Borah.

Now, we will download the script that installs the most current version of Anaconda. We will download this using wget:

wget -O - https://www.anaconda.com/distribution/ 2>/dev/null | sed -ne 's@.*\(https:\/\/repo\.anaconda\.com\/archive\/Anaconda3-.*-Linux-x86_64\.sh\)\">64-Bit (x86) Installer.*@\1@p' | xargs wget

Now, we will execute this bash script using bash:

bash Anaconda3-2021.05-Linux-x86_64.sh

Now, we will Install QIIME2 using conda. We will download a *.yml file using wget to do this:

wget https://data.qiime2.org/distro/core/qiime2-2021.4-py38-linux-conda.yml

# Use conda to create an environment:
conda env create -n qiime2-2021.4 --file qiime2-2021.4-py38-linux-conda.yml

# Optional cleanup
rm qiime2-2021.4-py38-linux-conda.yml

# Test to see if it works, using conda activate:
conda activate qiime2-2021.4
conda deactivate

5 QIITA

Many of the data sets we are working with are found on University of California San Diego’s site QIITA (https://qiita.ucsd.edu/). You can create an account here. Email Stephanie Galla stephaniegalla@boisestate.edu to ask her to add you to projects.