SbmlToSbol

Install

Install requirements

From PIP

From the console, type:

pip install --upgrade pip
pip install -r requirements.txt

From Conda

From the console, type:

conda update --all -y
conda env create -f environment.yml

Run

If dependencies have been installed within a conda environment, run:

conda activate sbml2sbol

or directly

conda run --name sbml2sbol <command>

where command is the one below.

Then, run in a terminal:

python -m sbml2sbol --input tests/data --outfile result.sbol

Docker

1. From the console, type bash docker/build.sh to build the Docker image.
2. To run, type bash docker/run.sh. The file docker/run.sh expect the following command line arguments:
   • input_folder The directory (with absolute path) containing in input files (in SBML format - essentially the output from Selenzyme).
   • outfile The output filename (with absolute path).
   • RBS (optional) Boolean flag, specifying whether an RBS site should be added to each gene (default: True).

Test

After installing pytest, run:

export PYTHONPATH=$PWD
pytest -v tests