Mercurial > repos > tduigou > get_sbml_model
view README.md @ 1:ceffb29b60c9 draft
planemo upload commit 9c19f737cd6e2152151c8bf97a53ab1afe51a4a0
author | tduigou |
---|---|
date | Mon, 03 Apr 2023 09:18:22 +0000 |
parents | |
children |
line wrap: on
line source
# get_sbml_model - Pick an SBML model among a list ## How to run get_sbml_model wrapper tests In order to execute tests on get_sbml_model wrapper, you need to: - Connect to your galaxy instance in interactive mode: ```bash docker exec -it -u root galaxy_galaxy_1 bash ``` - Copy all the contents of `test-data` folder into your own test-data directory which is located in your local galaxy instance : `/galaxy/test-data`. It contains all the input files and expected output files needed for the tests. - Install Planemo: You can see here the documentation for Planemo Installation : https://planemo.readthedocs.io/en/latest/installation.html Note that they recommand to install Planemo by setting up a virtual environment: ```bash python3 -m venv planemo . planemo/bin/activate pip install -U planemo ``` - run the tests: ```bash planemo test tools/synbiocad-galaxy-wrappers/get_sbml_model/wrap.xml ``` IMPORTANT: Maybe you will need to remove CONDA from your PATH for the command `planemo test` to run correctly. To do that, you can edit this file `~/.bashrc`, comment this line `PATH="/root/anaconda3/bin:$PATH"` and save changes. Planemo will output an html test summary `tool_test_output.html`.