Panoramic setup

Panoramic setup

The Panoramic package mainly consists of three Snakemake pipelines, which make use of a large number of tools and libraries. I made every effort to save you the mess of having to install all the required software by using Conda environments, so you only need to get conda to work before installing Panoramic.
Please note that panoramic is developed to run on a Unix environment, preferably with access to an HPC cluster.

Dependencies

Conda/Mamba

Conda is a popular package and environment manager. I recommend Miniconda (but Anaconda will work as well). Follow the instructions here to install it. Make sure that it is available for you to run from command line. Verify by running:
$ conda -V
Panoramic v1.2.0 was tested with conda 4.12.0, but slightly older or newer versions should work too. I also recommend installing Mamba, which provides quicker environment solving. Once conda is installed, simply run: conda install mamba -n base -c conda-forge

Installation

Once conda and/or mamba are installed, you can install Panoramic by following the steps below:

1. Clone the repository with current development code:
   $ git clone https://github.com/MayroseLab/Panoramic.git
2. To switch to the latest stable release, use:
   $ cd Panoramic
$ git checkout <version>, e.g. $ git checkout v1.2.0
3. Create the Panoramic environment:
   $ conda env create -f conda_env/snakemake.yml
   or
   $ mamba env create -f conda_env/snakemake.yml
4. Activate the environment (do this every time you want to run Panoramic):
   $ conda activate snakemake-panoramic

Testing you installation

To make sure everything works, it is highly recommended that you first try running the test data set before running your own data.