installing our tools - AstrobioMike/JPL-HBCU-2020 GitHub Wiki

One way we can install the programs we are going to be using is with the glorious package and environment manager conda (this comes installed already on our instances). If you're new to conda, I recommend going through the introduction to conda page on my site 🙂

The instance we want to run these programs on, and therefore that we are going to run these installation commands on, needs to be of size: "m1.xxlarge (CPU: 44, Mem: 120 GB, Disk: 60 GB)". The Managing and accessing our cloud computers page walks through the process of launching an instance.

conda create -y -n kraken2 -c conda-forge -c bioconda -c defaults kraken2=2.0.9beta bracken=2.6.0

Then we can enter the environment with:

conda activate kraken2

And exit it when we want with:

conda deactivate

conda create -y -n ganon -c conda-forge -c bioconda -c defaults ganon=0.2.3

Then we can enter the environment with:

conda activate ganon

And exit it when we want with:

conda deactivate

conda create -y -n centrifuge -c conda-forge -c bioconda -c defaults centrifuge=1.0.4_beta

Then we can enter the environment with:

conda activate centrifuge

And exit it when we want with:

conda deactivate