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install_conda.md

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How to download genome database

  1. Choose GENOME from hg19, hg38, mm9 and mm10 and specify a destination directory. 
    $ bash genome/download_genome_data.sh [GENOME] [DESTINATION_DIR]
  2. Find a TSV file on the destination directory and use it for "chip.genome_tsv" in your input JSON.

How to install pipeline's Conda environment

  1. Install Conda.

  2. Install Conda environment for pipeline.

$ conda/install_dependencies.sh
  1. Initialize Conda and re-login.
$ conda init bash
$ exit
  1. Configure pipeline's python2 and python3 environments.
$ conda/config_conda_env.sh
$ conda/config_conda_env_py3.sh
  1. Update pipeline's Conda environment with pipeline's python source code. You need to run this step everytime you update (git pull) this pipeline.
$ conda/update_conda_env.sh