RAxML-NG version comparison pipeline

Setup

Download the code:

git clone https://github.com/tschuelia/RAxML-NG-comparison.git

If you don't have miniconda already, install it according to the instructions [here] (https://docs.conda.io/en/latest/miniconda.html#installing)
Solving the environment using conda is very slow, so I recommend you to use [mamba] (https://github.com/mamba-org/mamba) instead. You can install mamba using conda:
```
conda install mamba
```
Create a new conda environment using the provided environment.yml file:
```
mamba env create -f environment.yml
```
Activate the conda environment:
```
conda activate comparison
```
Get all RAxML-NG versions you want to test ready to use.

Adjust the config.yaml file to your needs. The comments in the config.yaml will guide you.
Do a snakemake dry run to make sure everything works as expected:
```
snakemake -n -p
```
This will print all jobs that Snakemake will do.
Run the pipeline
```
snakemake --cores [number of cores*] -k -p
```
* you can either manually set a number of cores, or you can set --cores all and Snakemake will use all cores your system has.

Running the pipeline on a cluster is a bit more difficult, especially when we want to run it on multiple nodes. You can find detailed instructions on how to setup snakemake on a slurm cluster here.
Once the pipeline ran successfully, you can have a look at the results using an interactive Dash plotting website. You have to start the dash server manually:
```
python plots/index.py
```
If you ran the pipeline on you laptop, you can directly open http://127.0.0.1:8050/ in your browser. In case you ran it on a remote server you first have to do port forwarding to view the website:
```
ssh -L 8050:localhost:8050 [address of the server]
```