Many tools don’t require root privileges and can be installed in user space. This enables users to customize  Python packages to their needs, without conflicting with any system-level Python installations, or Python installations other users have performed.

A Miniconda Python installation is a common prerequisite for Python-based applications in machine learning and other fields.

Miniconda is a free software package that includes the condapackage and environment manager.

1. Download the Miniconda installer


2. Run the installer

$chmod 755 


3. Configuring Conda

$./conda update conda

 $./condaconfig --add channels bioconda

Miniconda installers contain the conda

package manager and Python

   $ condainstall numpy

Creating environments with Conda
  $ condainstall bwa 

Or a new environment can be created:

  $ condacreate -n aligners bwa bowtie hisatstar


Many HPC groups are using containers for their software. Some tools come as singularity or docker  images. 

(1) If there is no docker container available for your package you can build one in your local machine with the OS of your choice and install your package.
(2) Push the container to a cloud container repo. ie.
(3) Pull the docker container as a singularity image in juno, doing singularity pull docker://<your-image>
(4) Run your package by doing singularity run <your-image> <your-package-command>

Module avail will show you the available packages and versions.

You can use module to load singularity as:
module load singularity/3.7.1

Please read more about how to use containers.




If you would like to request help installing the software, please use this form here: