How to install pipeline's Conda environment

If you do not have miniconda (or anaconda) installed, follow the instructions below in steps 1 - 4 to install miniconda.

IF YOU ALREADY HAVE ANACONDA OR MINICONDA INSTALLED, SKIP TO STEP 5

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

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.
IMPORTANT: Disable auto activation of base Conda enrivonment.

$ conda config --set auto_activate_base false

IMPORTANT: Close your session and re-login.
Install pipeline's Conda environment. Add mamba to the install command line to resolve conflicts much faster.

$ bash scripts/uninstall_conda_env.sh  # uninstall it for clean-install
$ bash scripts/install_conda_env.sh mamba  # remove mamba if it does not work

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

=== All done successfully ===

Activate pipeline's Conda environment before running a pipeline.

$ conda activate encode-atac-seq-pipeline

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