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annotate README.md @ 10:db0138e42c19 draft

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planemo upload commit be50878b7e90467860bbe85aac55ea8e3507d1e5
author tduigou
date Thu, 20 Apr 2023 08:14:22 +0000
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1 # RetroPath2-wrapper -- Build a reaction network from a set of source compounds to a set of sink compounds.
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3 The open-source software package RetroPath2-wrapper is available here : https://github.com/brsynth/RetroPath2-wrapper
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5 ## How to run RetroPath2 wrapper tests
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7 In order to execute tests on RetroPath2 wrapper, you need to:
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9 - Connect to your galaxy instance in interactive mode:
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11 ```bash
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12 docker exec -it -u root galaxy_galaxy_1 bash
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13 ```
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14 - 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.
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16 - Install Planemo:
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17 You can see here the documentation for Planemo Installation : https://planemo.readthedocs.io/en/latest/installation.html
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18 Note that they recommand to install Planemo by setting up a virtual environment:
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20 ```bash
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21 python3 -m venv planemo
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22 . planemo/bin/activate
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23 pip install -U planemo
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24 ```
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26 - run the tests:
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28 ```bash
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29 planemo test --conda_channels conda-forge,brsynth --conda_debug tools/BRSynthTools/RetroPath2-wrapper/wrap.xml
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30 ```
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32 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.
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34 Planemo will output an html test summary `tool_test_output.html`.