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Software setup

What is conda?

Conda is a "package manager" or software installer. See the full list of commands.

conda install to install a package.

conda list to list installed packages.

conda search to search packages. Note that you'll see one package for every version of the software and for every version of Python (e.g. conda search sourmash).

What is bioconda?

See the bioconda paper and the bioconda web site.

Bioconda is a community-enabled repository of 3,000+ bioinformatics packages, installable via the conda package manager. It consists of a set of recipes, like this one, for sourmash, that are maintained by the community.

What problems does conda (and therefore bioconda) solve?

Conda tracks installed packages and their versions, and makes sure that different installed packages don't have conflicting dependencies. It makes software installation so much better!

Constructing and using multiple environments

A feature that we do not use much here, but that can be very handy in some circumstances, is different environments.

"Environments" are multiple different collections of installed software. There are two reasons you might want to do this:

  • first, you might want to try to exactly replicate a specific software install, so that you can replicate a paper or an old condition.
  • second, you might be working with incompatible software, e.g. sometimes different software pipelines need different version of the same software. An example of this is older bioinformatics software that needs python2, while other software needs python3.

Installing the software for this course

We already installed conda for you, but you will need to tell your terminal where to look for that software. You can do this by executing the following:

echo 'export PATH=/LUSTRE/apps/workshop/miniconda3/bin:$PATH' >> ~/.bashrc
echo 'export PATH=/LUSTRE/apps/workshop/transrate-1.0.3-linux-x86_64:$PATH' >> ~/.bashrc
source ~/.bashrc

After executing this, you should be able to run conda and look for software environments

To see the installed environments, run

conda info --envs

To activate the tara environment, which contains all software we'll use in the workshop, run

source activate tara

When you want to exit this environment later, you can execute source deactivate to return to the base env.

Finally --

Run 

~/works18

and then

source activate tara

so that we are all working on different distinct computers on the omica cluster.