How to create a new ngv circuit build

Preparation

  1. Load the necessary modules

module purge
module load archive/2021-05 python/3.8.3 cmake

  1. Create and source a virtual environment

python3.8 -m venv venv3.8
source venv3.8

  1. Install the ngv building pipeline

git clone https://bbpgitlab.epfl.ch/molsys/ArchNGV.git
cd ArchNGV/
make install

  1. Create an ngv circuit exemplar

ngv create-exemplar project_dir

Which will create the project_dir directory with a bioname folder, which includes default recipes for building an ngv circuit.

Running

The ngv command will appear to the path following the package installation. The ngv run command is a wrapper around snakemake with default preset options and arguments. It uses the same options and arguments as snakemake. For example:

ngv run --bioname /path/to/bioname --cluster-config /path/to/cluster.yaml

where the cluster.yaml is located inside the bioname folder for the exemplar above.

archngv/snakemake/Snakefile contains many ready to use recipes that allow you to generate any part of an ngv circuit. Such recipes are called phases in snakemake. Usually it is a name of a circuit file you want to generate. To choose a phase, type its name at the end of circuit-build run call. For example:

ngv run --bioname /path/to/bioname --cluster-config /path/to/cluster.yaml phase-name