example

Setup

1. clone this repository with git clone https://github.com/vanheeringen-lab/anansnake.git
2. cd into the anansnake directory
3. create a conda environment with anansnake (mamba create -n anansnake anansnake or mamba env create -n anansnake -f requirements.yaml)
4. activate the conda environment with mamba activate anansnake

Running anansnake on the example data

To check if everything is set up right, we can do a dry run:

anansnake --configfile example/config.yaml --resources mem_mb=48_000 --cores 12 --dry-run --reason

If you get an error, be sure to check the red text! I've added human-readable feedback where I could.

With the example data, you still need to provide a genome and gene annotation. You can download the GRCz11 genome and gene annotation with

genomepy install GRCz11 --annotation

If you do another dry run you should have no more errors, and see what is going to happen.

To do the real run, you need to specify how many cores you want to use, and how much RAM you have:

anansnake --configfile example/config.yaml --resources mem_mb=48_000 --cores 12