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Bioconda

bioconda

Description

Conda is a package management tool that is used to distribute and install software tools together with their dependencies. In Taito, the bioconda module takes in use a CSC maintained Conda environment (Python2 based miniconda2) together with channel settings that enable easy usage of the Bioconda repository.

The Bioconda environment is used for two purposes in Taito:

  1. Some software tools, maintained by CSC, are installed and used as conda environments.
  2. Taito users can use bioconda module to install tools, available in Bioconda repository, to their own personal Conda environments.

There is two versions of  Bioconda installation available in taito:

  • Python2.7 and miniconda2 based installation (2, default) that is taken in use with command:
module load bioconda
  • Python3.6 and miniconda3 based installation (3) that is taken in use with command:
module load bioconda/3

 


Available

Version on CSC's Servers

Conda/Bioconda versions 2 and 3 are available in Taito supercluster.


Usage

1. Using tools installed with bioconda

To use software environments that are installed to Taito using Conda (either by CSC or yourself),  first load bioconda module:

module load bioconda

or if you wish to use the miniconda3 based version:

module load bioconda/3

Then list the available Conda environments

conda env list

Next activate a Conda environment

source activate env_name

Later on you can deactivate the environment with command:

source deactivate

 

2. Installing software for your own use with bioconda

You can use the bioconda module to install software packages available in the Bioconda repository to your personal conda environments. In the example below a new conda environment, containing bedops package is cerated:

module load bioconda
conda create -n my_biotools bedops
source activate my_biotools

After this, commands included in bedops tools can be used. For example:

vcf2bed

To deactivate the current conda environment, run command:

source deactivate

Next time you need to use vcf2bed, it is enough that you run the set-up commands:

module load bioconda
source activate my_biotools
vcf2bed

Not that the miniconda2 and miniconda3 based environments are independent. If you have installed your application using Bioconda version 3 the environment is not available when the default bioconda 2 module is loaded (and vice versa).

 


Discipline

Biosciences

References


Support


Manual