Setting up Bioconda

Probably the easiest (but not the only) way to install some external tools required by PacBio Data Processing, like Pbindex, Blasr and CCS, is through conda. If you decide to follow this route, this section can hopefully help you.

The complete instructions can be found in PacBio & Bioconda and the links therein, but they basically amount to:

  1. Install conda. See installing conda for full details, but it is probably enough to use Miniconda, a minimal conda installer. In that case we will assume, as an example, that the conda environment is installed in a directory called:

    /home/dave/miniconda3
    

    Warning

    Depending on the choices made during the process of installing Miniconda you may allow the installer to configure your shell such that it always activates the conda environment at login time. If that is the case, and you are using Bash, you will find in your Bash initialization file , ~/.bashrc, a block similar to the following one:

    # >>> conda initialize >>>
    # !! Contents within this block are managed by 'conda init' !!
    __conda_setup="$('/home/dave/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
    if [ $? -eq 0 ]; then
        eval "$__conda_setup"
    else
        if [ -f "/home/dave/miniconda3/etc/profile.d/conda.sh" ]; then
            . "/home/dave/miniconda3/etc/profile.d/conda.sh"
        else
             export PATH="/home/dave/miniconda3/bin:$PATH"
        fi
    fi
    unset __conda_setup
    # <<< conda initialize <<<
    

    Since we are using the conda environment in a very limited way, you can comment that block, prepending a # to each line.

  2. Setup the channels in the conda environment just created as described in Bioconda.

Obviously, for the purpose of having PacBio Data Processing up and running, it is not necessary to install multiple conda environments to have Pbindex, Blasr and CCS. The three tools can be installed in the same conda environment.

Once the environment is created, if can be activated with:

source miniconda3/bin/activate

and deactivated with:

conda deactivate