Installation

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
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - 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

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