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ComputationalGenomicsManual

Robs manual for the computational genomics and bioinformatics class.

Installing software using CONDA

We are going to install all our software using conda and bioconda. First, we need to install conda:

Download conda

Head to the miniforge download page and download the appropriate installer.

You want :

Here is a quick way to download that script!

Right click on the appropriate link, and choose Copy link address. Go back to your terminal window (probably Putty) and type wget and a space, and then paste the URL that you just copied. Press return and it should download the file for you!

The file should be called Miniconda3-latest-Linux-x86_64.sh but in case it is not, just substitute the appropriate file name below. Remember that you can check with ls -ltr to see the newest file downloaded.

Run the miniconda installer:

bash Miniconda3-latest-Linux-x86_64.sh

This will ask you some questions, and you can pretty much accept the default answer to all the questions.

Once the installer has finished the best way to continue is to log out, and then log back in. This will reset your account and you will have conda activated. At the bottom left of your screen you should see it say (base) which means that you are in the base conda installation.

Install your first bioinformatics package

We are going to install fastp and test to see if it works. This will demonstrate how to install a conda package.

mamba install -c conda-forge -c bioconda fastp

Again, this will work on resolution of the packages for you and ask if you are sure. Once it is complete, you should be able to issue the command:

fastp -v

to see the version of fastp that has been installed.

You can also run

fastp -h

To get the full fastp help menu

Install snakemake

For the next steps of this tutorial, we are going to use snakemake to run some software. So we are going to use mamba to install that:

mamba install -c conda-forge -c bioconda snakemake

Once that has completed, snakemake -v should show you the current version.

Install other bioinformatics packages

You can install pretty much any bioinformatics package using conda. The anaconda website has a complete list and you can visit the bioconda page for more information about bioconda.

but to get started, you might want to install:

mamba install -c conda-forge -c bioconda fastp minimap2 samtools

Adding channels

It is a pain to keep typing -c conda-forge -c bioconda so we can just add those two channels to our configuration

conda config --add channels conda-forge
conda config --add channels bioconda

Updating a package

With conda (or mamba) you can easily update a package if there is a newer version. For example, to update snakemake you would use:

mamba update snakemake

What this means is the you are responsible for ensuring your software is up-to-date. Or not. If you are working on a set of data analyses you may want to keep all the software at the same version so that each time you do an analysis you get comparable answers. With conda, you have control over the update cycles, but don’t forget from time-to-time you might want to update the software!

Environments

If you want to keep different versions of software or run different pipelines you can do that with conda, in what are called environments. Each one can have different software. conda is clever, because if you have the same software in two different environments you don’t need an entire copy of the software. At this stage, you don’t need to worry about that, and you can just install everything in the base environment. But if you start to run into installation issues, then remember you can separate things into different environments.