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.
Bioconda is free to and open source under MIT License.
- Puhti: miniconda3 and miniconda2
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:
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:
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:
To deactivate the current Conda environment, run command:
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
You should not use conda init in Puhti. This applies to both Bioconda and your own Conda installations.
conda init modifyes your account so that it takes the Conda environment automatically in use. This is in principle handy, but in practice it will often cause problems when you try to use software that were not installed with your default Conda environment.
Last edited Mon Mar 29 2021