Setup Conda and Mapping Environment

Install conda from miniconda or anaconda.

Conda init

After installed conda, use conda init on your favorite shell
# e.g., bash or zsh
conda init bash
# you need to restart shell after conda init

Add channels

# run these command to add bioconda into your conda channel,
# the order of these 3 line matters
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

Create Environment With Required Packages

This command will create a conda environment called "mapping" and install all required packages for you. The mapping_env.yaml contains the detail about the environment, you can copy the content of that file below.
# conda is a bit slow, this step will take ~30 min in my server,
# but you only need to do this once.
conda env create -f mapping_env.yaml

Content of mapping_env.yaml file

name: mapping
- conda-forge
- bioconda
- defaults
- python=3.7
- pip
- jupyter
- jupyter_contrib_nbextensions
- cutadapt=2.10
- snakemake=5.17
- bismark=0.20
- samtools=1.9
- picard
- bedtools=2.29
- star=2.7.3a
- subread=2.0
- bowtie2=2.3
- bowtie=1.3
- htslib=1.9
- pysam=0.15
- pytables
- seaborn
- matplotlib
- pip:
- papermill

Activate the mapping environment

# enter env
conda activate mapping
# exit env
conda deactivate
Remember you need to run this command EVERY TIME before using the pipeline.

Install YAP and Allcools

Install YAP

# enter mapping env first
pip install cemba-data

Update YAP

# enter mapping env first
pip install --upgrade cemba-data

Install Allcools

# enter mapping env first
pip install allcools

Update ALLCools

# enter mapping env first
pip install --upgrade allcools