Feb 02, 2024

Public workspaceBacterial Genomics24

DOI
dx.doi.org/10.17504/protocols.io.x54v9pxpzg3e/v1
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Open access
DOI: dx.doi.org/10.17504/protocols.io.x54v9pxpzg3e/v1
Protocol Citation: George Odette 2024. Bacterial Genomics24. protocols.io https://dx.doi.org/10.17504/protocols.io.x54v9pxpzg3e/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: In development
We are still developing and optimizing this protocol
Created: February 02, 2024
Last Modified: February 02, 2024
Protocol Integer ID: 94622
Abstract
This is the protocol for going through the bacterial genomics course.
Installing software for the Bacterial Genomics24
Installing software for the Bacterial Genomics24
We will install many of the software we will use using conda.
Conda
To install conda, run the following script

Once the download is complete, run this script:

bash Anaconda3-2023.09-0-Linux-x86_64.sh
The first time you call conda you might get the error below:
conda: command not found
If that happens, run this script to add conda to path:

export PATH=~/anaconda3/bin:$PATH
But again, if you refresh the shell, you will bump into conda: command not found again. So, add the script to the bashrc file.
Open bashrc using
nano ~/.bashrc
The add the export PATH=~/anaconda3/bin:$PATH at the bottom of the file. Click ctrl + o, to save, press enter, the ctrl + x to exit.
Configuring bioconda
Run the following scripts to configure Bioconda

conda config --add channels defaults
conda config --add channels biocondac
onda config --add channels conda-forge