Multiome and visium data from the brain and heart of mice that went to space.
This pipeline uses Snakemake to ensure reproducibility.
Clone repo:
git clone git@github.com:saezlab/astromouse.git
cd astromouse
Install mamba (this might take a while) to install packages faster:
conda install -n base -c conda-forge mamba
Then create a new enviroment specific for Snakemake:
mamba create -c conda-forge -c bioconda -n snakemake snakemake
conda activate snakemake
Snakemake takes care of installing all dependencies to the environments. Set them up by running:
snakemake --conda-create-envs-only
You can see which steps will be executed by running:
snakemake -n
Run all steps necessary to reproduce the plots:
snakemake --use-conda -c 4 #will run on 4 local cores
For a cluster with SLURM as job manager:
snakemake --profile config/slurm -j 1 #will submit only one job at a time
More information about how to use and execute snakemake can be found in the snakemake tutorial