Mercurial > repos > tduigou > rp2paths
diff README.md @ 2:2452952f7bc2 draft
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
author | tduigou |
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date | Mon, 03 Apr 2023 08:15:46 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Mon Apr 03 08:15:46 2023 +0000 @@ -0,0 +1,34 @@ +# rp2paths -- Enumerate and seperate the different pathways generated by RetroPath2.0 + +The open-source software package rp2paths is available here : https://github.com/brsynth/rp2paths + +## How to run rp2paths wrapper tests + +In order to execute tests on rp2paths 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/rp2paths/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`. \ No newline at end of file