mulled: also consider non strict channel priority #19425
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for the creation of conda environments we try 1. strict channel priotity 2. if this fails try without https://github.com/galaxyproject/galaxy/blob/5f484fca6255fbbc8a66016601c3fcab20271c81/lib/galaxy/tool_util/deps/conda_util.py#L282 For the creation of mulled containers we don't do this. I stumbled over this a few times when creating containers for older tools, where a bioconda package was used that is now in conda-forge (and with strict priority only the newer conda-forge packages can be installed) Also restructured slightly. Before the `build` was appended to the `involucro_args` early. Therefore some inserts were needed in the middle of the list. Fix verbose option which was ignored before.
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nsoranzo
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Jan 21, 2025
Co-authored-by: Nicola Soranzo <[email protected]>
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container will need galaxyproject/galaxy#19425 this is because the used versions are from bioconda and are now masked (due to strict channel priority) by newer conda-forge packages ``` [Jan 21 12:47:26] SERR LibMambaUnsatisfiableError: Encountered problems while solving: [Jan 21 12:47:26] SERR - package perl-uri-1.71-pl526_3 is excluded by strict repo priority [Jan 21 12:47:26] SERR - package perl-text-csv-1.33-pl526_1 is excluded by strict repo priority [Jan 21 12:47:26] SERR - package perl-soap-lite-1.19-0 requires perl-io-socket-ssl, but none of the providers can be installed [Jan 21 12:47:26] SERR - package perl-html-template-2.95-0 requires perl-scalar-list-utils, but none of the providers can be installed ```
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for the creation of conda environments we try
see here.
For the creation of mulled containers we don't do this, yet. I stumbled over this a few times when creating containers for older tools, where a bioconda package was used that is now in conda-forge (and with strict priority only the newer conda-forge packages can be installed)
Also restructured slightly. Before the
buildcommand was appended to theinvolucro_argsearly. Therefore some inserts were needed in the middle of the list.Fix verbose option which was ignored before.
How to test the changes?
(Select all options that apply)
mulled-build-tool buildon https://github.com/workflow4metabolomics/wrapper-bank-massbank-spectrum_search/blob/dev_fg/massbank_ws_searchspectrum.xmlLicense