Installation

Setup Conda and Mapping Environment

Install conda from miniconda or anaconda.

Conda init

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

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# run these command to add bioconda into your conda channel,
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# the order of these 3 line matters
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conda config --add channels defaults
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conda config --add channels bioconda
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conda config --add channels conda-forge
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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.
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# conda is a bit slow, this step will take ~30 min in my server,
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# but you only need to do this once.
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conda env create -f mapping_env.yaml
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Content of mapping_env.yaml file

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

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

Install YAP and Allcools

Install YAP

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# enter mapping env first
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​
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pip install cemba-data
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Update YAP

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

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# enter mapping env first
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pip install allcools
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Update ALLCools

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# enter mapping env first
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pip install --upgrade allcools
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