Installation

Setup Conda and Mapping Environment

Install conda from miniconda or anaconda.

• IMPORTANT: select python 3

• miniconda (recommended)

• anaconda (larger)

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

Why using a conda environment?

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.

How to check whether you are in the mapping environment?

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