try to improve README.md for new contributors #296
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What didn't work ? |
mvdbeek
reviewed
Nov 23, 2023
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I did: $ planemo test --galaxy_url https://usegalaxy.eu --galaxy_user_key $(cat ~/switchdrive/galaxy_eu.txt) se-wgs-variation.ga
waiting for invocation 8704148c5c8a4c71
collecting outputs to directory /tmp/tmpe5pn36w9
galaxy.tool_util.verify INFO: ## files diff on '/home/ldelisle/Documents/mygit/iwc/workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/test-data/final_snpeff_annotated_variants.vcf' and '/tmp/tmpvgvlihhnfinal_snpeff_annotated_variants.vcf': lines_diff = 6, found diff = 362
None
galaxy.tool_util.verify INFO: ## files diff on '/home/ldelisle/Documents/mygit/iwc/workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/test-data/final_snpeff_annotated_variants.vcf' and '/tmp/tmp3ydoisp4final_snpeff_annotated_variants.vcf': lines_diff = 6, found diff = 362
NoneAnd then $ planemo workflow_test_on_invocation --galaxy_url https://usegalaxy.eu --galaxy_user_key $(cat ~/switchdrive/galaxy_eu.txt) se-wgs-variation-tests.yml 8704148c5c8a4c71
waiting for invocation 8704148c5c8a4c71
collecting outputs to directory /tmp/tmpeq9cw2ru
bioblend WARNING: GET: error 404: b'{"err_msg": "No such workflow found.", "err_code": 404001}', 9 attempts left
bioblend WARNING: GET: error 404: b'{"err_msg": "No such workflow found.", "err_code": 404001}', 8 attempts left
bioblend WARNING: GET: error 404: b'{"err_msg": "No such workflow found.", "err_code": 404001}', 7 attempts left
bioblend WARNING: GET: error 404: b'{"err_msg": "No such workflow found.", "err_code": 404001}', 6 attempts left
bioblend WARNING: GET: error 404: b'{"err_msg": "No such workflow found.", "err_code": 404001}', 5 attempts left
bioblend WARNING: GET: error 404: b'{"err_msg": "No such workflow found.", "err_code": 404001}', 4 attempts left
bioblend WARNING: GET: error 404: b'{"err_msg": "No such workflow found.", "err_code": 404001}', 3 attempts leftI was wondering if it was a bug or if it was me who did not know how to use it... |
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
lldelisle
commented
Dec 1, 2023
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Do you want to wait for the release of planemo before merging this? |
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I released planemo last week, 0.75.19 should work |
mvdbeek
approved these changes
Dec 14, 2023
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Attention: deployment skipped! https://github.com/galaxyproject/iwc/actions/runs/7212073352 |
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@mvdbeek would you mind to fill the
planemo workflow_test_on_invocationpart (I did not managed to make this command work...).