conda directory to $SCRATCH, you can create a new environment. You can create your own personal conda environment using miniconda which you can use to install conda and bioconda packages.īy default, miniconda will save environments in your $HOME/.conda directory but since space is limited in your $HOME directory, you will either need to move your $HOME/.conda directory to $SCRATCH or specify the full path of your miniconda environment. Then you can add packages to your bio environment # To deactivate an active environment, use: To to create an Anaconda conda environment called bio, do the following on the command line:Īfter your bio environment is created, you will see output on how to activate and use your bio environment You only need to do this step once in order to add the conda-forge and bioconda channels:Ĭonda config -set auto_activate_base False You can create more than one environment in case you need specific versions of tools.īefore you begin, you will need to contact the HPRC helpdesk to request a $SCRATCH file quota increase because creating a conda environment will add thousands of files to your $SCRATCH space.Īfter you get your file quota increase, the next thing you need to do is to add a few conda channels which contain certain bioinformatics tools.
Once you create a conda environment, you can continue to install other packages into that environment. You can install software that supports conda/bioconda installation inside the conda environment you create. You can create your own personal conda environment using Anaconda which installs conda and bioconda packages.
1.7 See available environments and installed packages.1.5 Relocate the default install directory.
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