Mercurial > repos > tduigou > rp2paths
comparison 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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| 1:e3db7fb2c85e | 2:2452952f7bc2 |
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| 1 # rp2paths -- Enumerate and seperate the different pathways generated by RetroPath2.0 | |
| 2 | |
| 3 The open-source software package rp2paths is available here : https://github.com/brsynth/rp2paths | |
| 4 | |
| 5 ## How to run rp2paths wrapper tests | |
| 6 | |
| 7 In order to execute tests on rp2paths wrapper, you need to: | |
| 8 | |
| 9 - Connect to your galaxy instance in interactive mode: | |
| 10 | |
| 11 ```bash | |
| 12 docker exec -it -u root galaxy_galaxy_1 bash | |
| 13 ``` | |
| 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. | |
| 15 | |
| 16 - Install Planemo: | |
| 17 You can see here the documentation for Planemo Installation : https://planemo.readthedocs.io/en/latest/installation.html | |
| 18 Note that they recommand to install Planemo by setting up a virtual environment: | |
| 19 | |
| 20 ```bash | |
| 21 python3 -m venv planemo | |
| 22 . planemo/bin/activate | |
| 23 pip install -U planemo | |
| 24 ``` | |
| 25 | |
| 26 - run the tests: | |
| 27 | |
| 28 ```bash | |
| 29 planemo test --conda_channels conda-forge,brsynth --conda_debug tools/BRSynthTools/rp2paths/wrap.xml | |
| 30 ``` | |
| 31 | |
| 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. | |
| 33 | |
| 34 Planemo will output an html test summary `tool_test_output.html`. |