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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
author metexplore
date Wed, 17 May 2023 13:26:37 +0000
parents ae4c301919c4
children 1436e9cde9c9
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1 # How to build wrappers for new met4j-toolbox apps? 1 # How to build wrappers for new met4j-toolbox apps?
2 2
3 ## Install planemo 3 ## Install planemo
4 4
5 ```console 5 ```console
6 virtualenv --python=/usr/bin/python3.8 .venv; 6 pip install virtualenv
7 source .venv/bin/activate 7 python -m virtualenv planemo
8 . planemo/bin/activate
9 pip install --upgrade pip setuptools
8 pip install planemo 10 pip install planemo
9 ``` 11 ```
10 12
11 ## Install singularity 13 ## Install singularity
12 14
13 Doc [Here](https://github.com/sylabs/singularity/blob/main/INSTALL.md). 15 Doc [Here](https://github.com/sylabs/singularity/blob/main/INSTALL.md).
14 16
15 ## Create new wrappers 17 ## Create new wrappers
16 18
17 1. Create a branch (e.g. newFeature) (or a new release) in met4j and develop your apps 19 - Create a branch (e.g. newFeature) (or a new release) in met4j and develop your apps
18 2. Push the branch 20 - Push the branch
19 3. If this branch is not master or develop, launch manually the 21 - If this branch is not master or develop, launch manually the
20 building of the singularity image in the met4j CI-CD (this singularity image will be downloaded by the galaxy instance) 22 building of the singularity image in the met4j CI-CD (this singularity image will be downloaded by the galaxy instance)
21 4. Create a branch with the same name in met4j-galaxy (e.g. newFeature) 23 - Create a branch with the same name in met4j-galaxy (e.g. newFeature)
22 5. Use the GenerateGalaxyFiles of the met4j-toolbox (be careful, it must be the version of the new branch) to generate the wrappers for the new met4j apps. Or you can use the singularity image created in the third step. 24 - Use the GenerateGalaxyFiles of the met4j-toolbox (be careful, it must be the version of the new branch) to generate the wrappers for the new met4j apps. Or you can use the singularity image created in the third step.
23 25
24 ```console 26 ```console
25 met4j-toolbox.sif GenerateGalaxyFiles \ 27 met4j-toolbox.sif GenerateGalaxyFiles \
26 -o /path/to/met4j-galaxy/tools \ 28 -o /path/to/met4j-galaxy/tools
27 -v newFeature
28
29 ``` 29 ```
30 30
31 Where newFeature is the name of the new branch. 31 ## Write tests
32 32
33 6. Edit manually the wrappers where the tests are lacking. 33 - Edit manually the wrappers where the tests are lacking.
34 34
35 [Here](https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-tests) is the documentation about tests in galaxy 35 [Here](https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-tests) is the documentation about tests in galaxy
36 36
37 Put the test files in a test-data directory in the tool directory. 37 Put the test files in a test-data directory in the tool directory.
38 If the file is used in several tests, put it in the data directory at the root of the project and create a symbolic link in the test-data directory. 38 If the file is used in several tests, put it in the data directory at the root of the project and create a symbolic link in the test-data directory.
39 39
40 7. Check the syntax of the wrappers 40 ## Check the syntax of the wrappers
41 41
42 ```console 42 ```console
43 source .venv/bin/activate 43 . planemo/bin/activate
44 planemo shed_lint --tools \ 44 planemo shed_lint --tools \
45 --ensure_metadata \ 45 --ensure_metadata \
46 --urls \
47 --report_level warn \ 46 --report_level warn \
48 --fail_level error \ 47 --fail_level error \
49 --recursive tools 48 --recursive tools
50 ``` 49 ```
51 50
52 8. Launch the tests 51 ## Find apps without tests
52
53 ```console
54 python ./findToolsWithoutTests.py build/tools/
55 ```
56
57 ## Launch the tests
58
59 ### Build with a version number
60
61 To test your apps, you need to fill the good version of met4j singularity in each xml wrapper. For this, use this command:
62
63 ```bash
64 ./build.sh $versionNumber
65 ```
66
67 Where $versionNumber must correspond to the version of the met4j singularity instance created above.
68
69 ### Launch the tests on the built instance
53 70
54 Launching all the tests can be very time consuming. 71 Launching all the tests can be very time consuming.
55 72
56 You can launch the test for one tool (here convert.Sbml2Graph): 73 You can launch the test for one tool (here convert.Sbml2Graph):
57 74
58 ```console 75 ```console
59 source .venv/bin/activate 76 . planemo/bin/activate
60 planemo test \ 77 planemo test \
61 --galaxy_source https://github.com/galaxyproject/galaxy \
62 --galaxy_branch release_22.01 \
63 --job_config_file config/job_conf.xml \ 78 --job_config_file config/job_conf.xml \
64 tools/convert/Sbml2Graph/ 79 build/tools/Sbml2Graph/
65 ```
66
67 or for an entire package (here convert):
68
69 ```console
70 source .venv/bin/activate
71 planemo test \
72 --galaxy_source https://github.com/galaxyproject/galaxy \
73 --galaxy_branch release_22.01 \
74 --job_config_file config/job_conf.xml \
75 tools/convert/Sbml2Graph/
76 ``` 80 ```
77 81
78 If you want to test all the tools: 82 If you want to test all the tools:
79 83
80 ```console 84 ```console
81 source .venv/bin/activate 85 . planemo/bin/activate
82 planemo test \ 86 planemo test \
83 --galaxy_source https://github.com/galaxyproject/galaxy \ 87 --job_config_file config/job_conf.xml \
84 --galaxy_branch release_22.01 \ 88 build/tools/*
85 --job_config_file config/job_conf.xml
86 ``` 89 ```
87 90
88 The results of the tests can be read in tool_test_output.html. 91 The results of the tests can be read in tool_test_output.html.
89 92
90 9. If all the tests are ok, merge the new met4j branch in develop 93 ## Create new release
91 10. Create a new met4j release and finish the release: it will create a new singularity image for this version
92 11. Launch once again GenerateGalaxyFiles
93 94
94 ```console 95 When tests are ok, you can create a new met4j release. The CI will create a new Singularity image corresponding to this version.
95 met4j-toolbox.sif GenerateGalaxyFiles \ 96
96 -o /path/to/met4j-galaxy/tools \ 97 Create a new met4j-galaxy release with the same version number as met4j. After push, the CI will test again the apps. If it's ok, a new version of met4j-galaxy will be pushed on the galaxy toolshed. The instance in usegalaxy.fr will be updated the next monday.
97 -v 1.1.1 98
99 ## Update met4j-galaxy-runner
100
101 Docker image to run planemo on ci.
102
103 Creation du docker pour lancer galaxy et planemo :
104
105 ```bash
106 sudo docker login
107 sudo docker build -t metexplore/met4j-galaxy-runner:latest .
108 sudo docker push metexplore/met4j-galaxy-runner:latest
98 ``` 109 ```
99 110
100 where 1.1.1 is the number of the new release 111 <https://hub.docker.com/r/metexplore/met4j-galaxy-runner>
101
102 12. In met4j-galaxy, launch planemo lint to check if there is app without test and if everything is ok
103 13. Test all the tools
104 14. Merge on develop, create a new release, and push
105
106 This will test again all the tools on the gitlab CI/CD. If it's ok, a new version of met4j-galaxy will be pushed on the galaxy toolshed. The instance in usegalaxy.fr will be updated the next monday.