Mercurial > repos > tduigou > retropath2
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author | tduigou |
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date | Thu, 20 Apr 2023 12:30:18 +0000 |
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# RetroPath2-wrapper -- Build a reaction network from a set of source compounds to a set of sink compounds. The open-source software package RetroPath2-wrapper is available here : https://github.com/brsynth/RetroPath2-wrapper ## How to run RetroPath2 wrapper tests In order to execute tests on RetroPath2 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 --conda_channels conda-forge,brsynth --conda_debug tools/BRSynthTools/RetroPath2-wrapper/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`.