Last Updated: 12/06/2022
This is not an official PacBio GitHub repo. The scripts here are being actively developed. Use at your own risk.
- Python 3.7
- R
Python libaries required:
R packages required:
- ggplot2
- dplyr
- grid
- gridExtra
You can directly download/clone the repo to use the scripts directly.
$ git clone https://github.com/Magdoll/AAV.git
You can install the dependencies on your own or use one of the following conda-based options.
conda install -c bioconda pysam
conda install -c r ggplot2
conda install -c r dpylr
conda install -c r grid
conda install -c r gridExtra
Suppose you have anaconda installed and the binary is in $HOME/anaCogentPy37/bin
. You would add the binary to $PATH and create a new conda environment called AAV.env
.
$ export PATH=$HOME/anaCogentPy37/bin:$PATH
$ conda env create -f AAV.conda_env.yml
$ source activate AAV.env
At this point the prompt should change to (AAV.env) $
Please read the AAV tutorial