This pipeline is dependent on conda.

Step 1: Download and install miniconda3

First you need to download and install miniconda3:

for linux

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

for mac os

curl https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o Miniconda3-latest-MacOSX-x86_64.sh
bash Miniconda3-latest-MacOSX-x86_64.sh

Step 2: Clone the workflow

Clone the worflow

git clone https://github.com/Hoohm/dropSeqPipe.git

Step 3: Install snakemake

conda install -c bioconda -c conda-forge snakemake

Next step is config files completion

Complete the config.yaml with the missing information

UPDATES: How to update the pipeline

Go to your experiment folder, then pull.

git pull https://github.com/Hoohm/dropSeqPipe.git

If you want to update files/plots based on the updates you can use this command:

snakemake -R `snakemake --list-codes-changes`

This will update all the files that would be modified by the changes in the code (rules or script). Depending on how much and where the changes have been made, this might rerun the whole pipeline.