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Some Miniconda

Many tools don’t require root root privileges , and will let you customize your and can be installed in user space. This enables users to customize  Python packages to your 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.Below is the insurrections of how to install miniconda in your lab directory:

https://its.tntech.edu/display/MON/Installing+Miniconda+in+Your+HPC+Account

Some tools came with singularity image. Please read more about how to use singularity container. You can use module to load singularity as:
Module avail

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Miniconda is a free software package that includes the condapackage and environment manager. https://docs.conda.io/en/latest/miniconda.html

1. Download the Miniconda installer

wget  https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

2. Run the installer

$chmod 755 Miniconda3-latest-Linux-x86_64.sh 

$./Miniconda3-latest-Linux-x86_64.sh 

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

Containers

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. https://hub.docker.com
(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.

docker 

https://docker-curriculum.com/

singularity

https://sylabs.io/guides/3.5/user-guide/introduction.html

https://singularity.lbl.gov/quickstart

http://mskcchpc.org/display/CLUS/Singularity+Usage

If you would like to request help installing the software, please use this form here: http://hpc.mskcc.org/software-installation-request/