Installation

Main environment

Clone the repository, create the managed environment, and install the package:

git clone https://github.com/prangelab/omnomnomics.git
cd omnomnomics
micromamba env create -f environment.yml
micromamba activate omnomnomics
python -m pip install -e .

The supplied environment is the supported source of Snakemake and workflow tool versions. Omnomnomics does not require a conda executable for rule execution; the environment is created and activated with Micromamba before the controller is submitted.

Optional companion environments

Default narrow ATAC/ChIP analysis uses IDR. Install its isolated helper environment once:

bash scripts/install_idr_helper.sh

SPP cross-correlation QC is optional and uses a second helper environment:

bash scripts/install_spp_helper.sh

Both installers expose wrappers to the main environment. Normal runs still only require micromamba activate omnomnomics.

Differential Explorer only

For local inspection of completed differential-analysis outputs without the HPC toolchain:

micromamba env create -f environment.explorer.yml
micromamba activate omnomnomics-explorer
python -m pip install --no-deps --no-build-isolation .
omnomnomics-de-app --project-dir /path/to/project_or_DE_calling

Use environment.explorer.yml from the same release that produced the results.

Site configuration

Copy the packaged template to the user configuration directory and edit the cluster-specific values:

mkdir -p "${XDG_CONFIG_HOME:-$HOME/.config}/omnomnomics"
cp src/omnomnomics/workflow/config/site.yaml \
  "${XDG_CONFIG_HOME:-$HOME/.config}/omnomnomics/site.yaml"

The search order is:

  1. --site-config PATH
  2. $XDG_CONFIG_HOME/omnomnomics/site.yaml
  3. ~/.config/omnomnomics/site.yaml
  4. the packaged site defaults

The packaged cluster defaults target the SURF Snellius national supercomputer. Before running on another HPC system, review Configuration and provide a site configuration for that environment.