Mercurial > repos > tduigou > rrparser
comparison README.md @ 3:dd0dfd2cb8a8 draft
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author | tduigou |
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date | Mon, 03 Apr 2023 11:37:18 +0000 |
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1 # RRulesParser Galaxy wrapper | |
2 | |
3 The open-source software package RRulesParser is available here : https://github.com/brsynth/RRParser | |
4 | |
5 ## Installing | |
6 | |
7 * Create a new section in the Galaxy config file `config/tool_conf.xml` and paste the following: | |
8 ``` | |
9 <section id="sbc-rs" name="SynBioCAD RetroSynthesis"> | |
10 <tool file="synbiocad-galaxy-wrappers/RRulesParser/wrap.xml" /> | |
11 </section> | |
12 ``` | |
13 | |
14 * Make sure that the following entry exists under Galaxy's destination tag in `config/job_conf.xml`: | |
15 ``` | |
16 <destination id="local" runner="local" /> | |
17 ``` | |
18 | |
19 And that the destination of the tool is referred under the tools tag in `config/job_conf.xml`: | |
20 | |
21 ``` | |
22 <tool id="RRulesParser" destination="local" /> | |
23 ``` | |
24 | |
25 ## How to run RRulesParser wrapper tests | |
26 | |
27 In order to execute tests on RRulesParser wrapper, you need to: | |
28 | |
29 - Connect to your galaxy instance in interactive mode: | |
30 | |
31 ```bash | |
32 docker exec -it -u root galaxy_galaxy_1 bash | |
33 ``` | |
34 - 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. | |
35 | |
36 - Install Planemo: | |
37 You can see here the documentation for Planemo Installation : https://planemo.readthedocs.io/en/latest/installation.html | |
38 Note that they recommand to install Planemo by setting up a virtual environment: | |
39 | |
40 ```bash | |
41 python3 -m venv planemo | |
42 . planemo/bin/activate | |
43 pip install -U planemo | |
44 ``` | |
45 | |
46 Upgrade pip if needed. | |
47 | |
48 - run the tests: | |
49 | |
50 ```bash | |
51 planemo test --conda_channels conda-forge tools/synbiocad-galaxy-wrappers/RRulesParser/wrap.xml --biocontainers --no_conda_auto_init | |
52 ``` | |
53 | |
54 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. | |
55 | |
56 Planemo will output an html test summary `tool_test_output.html`. | |
57 | |
58 ## Built With | |
59 | |
60 * [Galaxy](https://galaxyproject.org) - The Galaxy project | |
61 | |
62 | |
63 ## Authors | |
64 | |
65 * Melchior du Lac | |
66 * Joan Hérisson | |
67 * Thomas Duigou | |
68 | |
69 ## License | |
70 | |
71 This project is licensed under the MIT License - see the [LICENSE.md](LICENSE.md) file for details |