Bioconda

Conda is a package management tool that is used to distribute and install software tools together with their dependencies. In Puhti, the bioconda module takes in use a CSC maintained Conda environment (Python3 based miniconda3) together with channel settings that enable easy usage of the Bioconda repository.

The Bioconda environment is used for two purposes in Puhti:

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

Available

  • Puhti: miniconda3 and miniconda2

Usage

1. Using tools installed with bioconda

To use software environments that are installed to Puhti using Conda (either by CSC or yourself), first define environment variable PROJAPPL to point to a directry of the project that you wish to use for your own conda environments.

Typically this is your /projappl/project_name directory, but you can use scratch too. This definition is made with command export . For example for project_012345 the command would be:

export PROJAPPL=/projappl/project_12345

Next, load bioconda module:

module load bioconda

This load miniconda3 based conda environment that is compatible with Python3 and gcc 7.4.0. If you wish to use Python2 based miniconda2, set up the conda environment with:

module load bioconda/2

Then you can list the available Conda environments

conda env list

And activate a Conda environment

source activate env_name

Later on you can deactivate the environment with command:

conda deactivate

2. Installing software for your own use with bioconda

You can use the bioconda module to install software packages available in the Bioconda and other conda repositories to your personal Conda environments. Not that you can't install new Conda packages to the base environment of bioconda, but you must create your own conda environment for installations.

In the example below a new Conda environment, containing bedops package is created:

export PROJAPPL=/projappl/project_xxxxxx
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:

conda deactivate

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

export PROJAPPL=/projappl/project_xxxxxx
module load bioconda
source activate my_biotools
vcf2bed

Support

servicedesk@csc.fi

Manual