Mercurial > repos > kls286 > chap_test_20230328
comparison Galaxy.md @ 0:cbbe42422d56 draft
planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
| author | kls286 |
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| date | Tue, 28 Mar 2023 15:07:30 +0000 |
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| -1:000000000000 | 0:cbbe42422d56 |
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| 1 # Install Planemo | |
| 2 ``` | |
| 3 python -m venv planemo | |
| 4 . planemo/bin/activate | |
| 5 pip install planemo | |
| 6 ``` | |
| 7 | |
| 8 ### Initialize chap.xml | |
| 9 ``` | |
| 10 planemo tool_init --id 'chap' --name 'CHESS Analysis Pipeline' --example_command 'runner.py --config config.yaml' --example_input config.yaml --cite_url 'https://github.com/CHESSComputing/ChessAnalysisPipeline' --help_from_command 'runner.py --help' --test_case --example_output data.out | |
| 11 ``` | |
| 12 this command will output: | |
| 13 ``` | |
| 14 Tool written to chap.xml | |
| 15 No test-data directory, creating one. | |
| 16 Copying test-file config.yaml | |
| 17 ``` | |
| 18 | |
| 19 Perform linting: | |
| 20 ``` | |
| 21 planemo l | |
| 22 Linting tool /Users/vk/Work/CHESS/ChessPipeline/chap.xml | |
| 23 Applying linter tests... CHECK | |
| 24 .. CHECK: 1 test(s) found. | |
| 25 Applying linter output... CHECK | |
| 26 .. INFO: 1 outputs found. | |
| 27 Applying linter inputs... CHECK | |
| 28 .. INFO: Found 2 input parameters. | |
| 29 Applying linter help... CHECK | |
| 30 .. CHECK: Tool contains help section. | |
| 31 .. CHECK: Help contains valid reStructuredText. | |
| 32 Applying linter general... CHECK | |
| 33 .. CHECK: Tool defines a version [0.1.0+galaxy0]. | |
| 34 .. CHECK: Tool defines a name [CHESS Analysis Pipeline]. | |
| 35 .. CHECK: Tool defines an id [chap]. | |
| 36 .. CHECK: Tool specifies profile version [21.05]. | |
| 37 Applying linter command... CHECK | |
| 38 .. INFO: Tool contains a command. | |
| 39 Applying linter citations... CHECK | |
| 40 .. CHECK: Found 1 likely valid citations. | |
| 41 Applying linter tool_xsd... CHECK | |
| 42 .. INFO: File validates against XML schema. | |
| 43 ``` | |
| 44 | |
| 45 Now, we can start server via the following commad: `planemo s`, | |
| 46 it will take a while. Once finished we may visit | |
| 47 `http://127.0.0.1:9090` to see our galaxy hub along with | |
| 48 our pipeline tool. |