How to install software on the exercise server

Using the conda package manager

conda is a cross-platform package manager that can install both full programs, as well as Python and R libraries for you, without the need for administrative privileges. (If you’ve used Linux before, it’s similar to apt.)

Many standard bioinformatics tools have been published for conda, most notably on the “bioconda” channel (list of packges). See here for more info about bioconda and conda in general.

Environment

While it’s possible to intall packages globally, for all users, that quickly leads to problems and clashes in software versions.

Therefore, you should create your own work environment where you can install the software you need.

Run the following (from anywhere), replacing test_fburic with the name you want. Since on this server the environments are visible and accessible for everyone, please add a unique identifier (e.g. “stX” for student X) in the name to avoid accidentally using the same name as your colleagues (e.g. test_st3)

conda create --name test_fburic

To see a list of environemnts, run:

conda env list

To activate (start using) the environment, run:

source activate test_fburic

You will see a (test_fburic) to the left of your prompt. You are now in that environment and anything you install will only be usable inside here.

Note: You will have to re-activate the environment every time you log in. (You can add the command at the end of your .bashrc file to have it executed on each login)

Further reading

See the documentation about managing environments

Software installation

Alternatives:

  1. The typical way is to google the tool you need and check if they provide instructions for conda
  2. If not, somebody else may have published it on a conda channel, so goole “ conda"
  3. Search for that package on the Bioconda list: https://anaconda.org/bioconda/repo or, failing that, on (Ana)conda globally: https://anaconda.org/ 3.5. You can also search from command line: conda search <software>

Example 1

Let’s install the cufflinks RNA-seq assembler. On their webpage they don’t list conda.

So, alternative 2. Googling for “cufflinks assembly conda” sent me to the listing of the package on the bioconda channel: https://anaconda.org/bioconda/cufflinks

So, the command to install it is:

 conda install -c bioconda cufflinks

Example 2

Let’s install STAR. It’s a standard tool so we expect it’s on bioconda.

conda install -c bioconda star

will just work.

Otherwise, we could have run a seach:

conda search star

Software installtion 2 - getting different versions

You may require a specific version (to reproduce results, other limitations) Running the conda search command or browsing online will list available version. If you search online, make sure the package has a Linux (pengion) logo. The search command only shows you what’s availalbe on the machine you’re on.

Example 3

If you for whatever reason want version 2.4.0j of star, run

conda install -c bioconda star==2.4.0j

Managing packages

For more operations, see the conda package management docs