Conda

conda installs: This is the future

Conda on Marvin on a per user basis, so you have total control over it. Log in and from the command line type Only ever do this once or you will get error pessages):

install-bioconda

Either log out and back in, or type:

source ~/.bashrc

This will make a user specific version of conda avible to you.

To find the package you want, search here:

https://bioconda.github.io/conda-recipe_index.html

or google search: - as there are multiple channels!!

conda name_of_tool_you_want

We strongly advise using environments: You can do this in many ways. Please see the link for more details (here you can specifiy exact version etc ..)

https://conda.io/docs/user-guide/tasks/manage-environments.html 

The easiest usage would be: e.g.

conda create -n NAME_OF_ENV PACKAGE_TO_INSTALL

This is an example of a toold called roary

conda create -n roaryENV roary

once it has installed, you can activate the environment by typing:

conda activate roaryENV

As a lot of tools have dependencies, all the dependencies should be installed during this process. It is a good idea to keep them looked up in their own ENV, so they dont interfere with dependencies and spcific version required for other things you have installed.

To get the latest version

conda update roary

You are now ready to use this package.

conda deactivate        to leave this environment.

If you want to install a specific version of a tool (use the equals sign and the version you want):

conda create -n samtools1.3 samtools=1.3

or

conda create -n python27 python=27

once you have this version of python installed, you can easily use (after you have activated the python env:

pip install biopython   (or whatever you require)

conda and perl Firstly, perl is a pain to look after. The way the cluster has been historically set up, all perl versions and modules are different on all the nodes. The new cluster will not be like this. Therefore, we cannot install modules for every user on all the nodes. What we recommend is you having you own perl version using conda:

conda create -n perlEnv perl

conda activate perlEnv

then install the modules you want

http://www.cpan.org/modules/INSTALL.html

cpan App::cpanminus

cpanm Term::ReadKey

Bioperl is difficult to install. Fact. But someone has put this in coda. So lets use that:

conda create -n bioperlEnv perl-bioperl

To list all the environments you have created:

conda info –envs

installing packages: https://bioconda.github.io/conda-recipe_index.html