Conda

WIP for progressing to user-centric conda installs

Dear Cosmika,

We are testing Bioconda on Marvin on a per user basis, so you have total control over it. Would you please be our first actual user test? The default python in /usr/bin is python 2.6 which is too old. As a warning, running the following will update this to 2.7 and 3.7. So, only do so if you do not specifically require the python 2.6 version for your other work. Although, you could set up a conda environment with 2.6 if you really wanted. I can’t think of anything that requires 2.6.

Log in and from the command line type:

install-bioconda

Either log out and back in or type: source ~/.bashrc

We strongly advise using environments: https://conda.io/docs/user-guide/tasks/manage-environments.html . You can do this in many ways. Please see the link for more details (here you can specifiy eact version etc ..). The easiest usage would be: e.g. conda create -n NAME_OF_ENV PACKAGE_TO_INSTALL

conda create -n roary roary

conda activate roary

conda update roary

You are now ready to use this package.

Conda deactivate to leave this environment.

This works for me and a test user. But may fail for you, so be patient with us.

To list all the environments you have created:

conda info –envs

installing packages: https://bioconda.github.io/recipes.html

Please let me know how you get on, and tell me of any errors.

Regards,

Peter Thorpe