Installation

You have two ways of installing the dependencies.

With miniconda

Step1: 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 repo

Clone the worflow to the folder where you run your pipelines

git clone https://github.com/Hoohm/CITE-seq-Count.git

Step 3: Create an environment based on environment.yaml

cd CITE-seq-Count
conda env create --name CITE-seq-Count --file environment.yaml

You can now run the script

Run the script with the missing information