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How to install pipeline's Conda environment

IMPORTANT: DO NOT USE A GLOBALLY INSTALLED CONDA. INSTALL YOUR OWN MINICONDA3 UNDER YOUR HOME DIRECTORY BY FOLLOWING THE INSTRUCTION HERE.

WARNING: DO NOT SKIP ANY OF THE FOLLOWING STEPS OR PIPELINE'S ENVIRONMENT WILL BE MESSED UP WITH YOUR LOCAL PYTHON/GLOBAL CONDA.

  1. MacOS users: MAKE SURE THAT YOU HAVE GNU grep INSTALLED ON YOUR SYSTEM. Check if your grep has a -P parameter.
$ grep --help  # check if a parameter "-P" exists
  1. Download Miniconda installer. Use default answers to all questions except for the first and last.
$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ bash Miniconda3-4.6.14-Linux-x86_64.sh

Type yes to the first question.

Do you accept the license terms? [yes|no]
[no] >>> yes

Type yes to the last question.

Do you wish the installer to initialize Miniconda3
by running conda init? [yes|no]
[no] >>> yes

  1. IMPORTANT: Close your session and re-login. If you skip this step then pipeline's Conda environment will be messed up with base Conda environment.

  2. IMPORTANT: Disable auto activation of base Conda enrivonment.

$ conda config --set auto_activate_base false

  1. IMPORTANT: Close your session and re-login.

  2. Install pipeline's Conda environment.

$ bash scripts/uninstall_conda_env.sh  # uninstall it for clean-install
$ bash scripts/install_conda_env.sh

WARNING: DO NOT PROCEED TO RUN PIPELINES UNTIL YOU SEE THE FOLLOWING SUCCESS MESSAGE OR PIPELINE WILL NOT WORK.

=== All done successfully ===
  1. Activate pipeline's Conda environment before running a pipeline.
$ conda activate encode-chip-seq-pipeline

$ caper run ...
$ caper server ...