From the console, type:
pip install --upgrade pip
pip install -r requirements.txt
From the console, type:
conda update --all -y
conda env create -f environment.yml
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
bash docker/build.sh
to build the Docker image.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).After installing pytest
, run:
export PYTHONPATH=$PWD
pytest -v tests