Therefore some of these tools are a treasure chest of cools tools, which can save many hours and kg of pain in installation process.Ĭonda create -n python36_bioperl python=3.6 perl-bioperl mummer scipy numpy biopython matplotlib To list all the dependencies you have within an envįor example, trinity comes with jellyfish, which can be difficult to install. To list all the environments you have created (you will forget the envs after a while, so name them well!!): What we recommend is you having you own perl version using conda:īioperl is difficult to install. Therefore, we cannot install modules for every user on all the nodes. The way the cluster has been historically set up, all perl versions and modules are different on all the nodes. Pip install biopython (or whatever you require)įirstly, perl is a pain to look after.

Once you have this version of python installed, you can easily use (after you have activated the python env: If you want to install a specific version of a tool (use the equals sign and the version you want):

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.Ĭonda deactivate to leave this environment. Once it has installed, you can activate the environment by typing:Īs a lot of tools have dependencies, all the dependencies should be installed during this process. This is an example of a toold called roary )Ĭonda create -n NAME_OF_ENV PACKAGE_TO_INSTALL Please see the link for more details (here you can specifiy exact version etc. We strongly advise using environments: You can do this in many ways. Or google search: - as there are multiple channels!! To find the package you want, search here: This will make a user specific version of conda avaible to you. Log in and from the command line type Only ever do this once or you will get error pessages):

Conda on Marvin on a per user basis, so you have total control over it.

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