Before Conda, life in bioinformatics for the beginner was hell. Now it is just a little less hellish because installing software packages and dependencies has a somewhat turn key solution.
Conda is open source and can run on the HPC or your local machine.
Many of the software packages you use will have many dependencies (other software packages). As new versions of software are released, they might have updated depenencies on newer versions of other software. It is convenient to have different environments that one can use for a particular suite of analysis tools. Or even environments that are used for just one (annoying and finnicky) tool.
You can follow these instructions to install [conda]https://docs.conda.io/projects/conda/en/latest/user-guide/install/macos.html on your Mac.
For working installing conda on your home directory of the HPC. Installation instructions for conda install in linux
Here is a conda installation tutorial
** I need to make sure that this installation works on the HPC. It was a long time ago that I did it myself **
There is a lot to learn regarding conda, but here is a cheatsheet that is helpful.
So assuming conda is installed, let’s create a new environment to use for running deeptools
conda create --name MyDeeptoolsEnv
“MyDeeptoolsEnv” is a lot of letters. You can call your environments whatever you want.
Assuming this goes smoothly, you can then activate the envinroment.
conda activate MyDeeptoolsEnv
Now we need to install bioconda. more info on bioconda here
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strictOk, with bioconda set up on our “MyDeeptoolsEnv” we can now actually install deeptools
conda install -c bioconda deeptools
Now we are ready to run deeptools! You can find a usage of deeptools in the short read RNA-Seq Tutorial