mulled: also consider non strict channel priority #19425
+41
−14
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
bernt-matthias
force-pushed
the
mulled_strict
branch
from
6b3bc4f to
530faee
Compare
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.
bernt-matthias
force-pushed
the
mulled_strict
branch
from
530faee to
b1a1f1d
Compare
nsoranzo
reviewed
Jan 21, 2025
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
bernt-matthias
added a commit
to bernt-matthias/xcms
that referenced
this pull request
Jan 21, 2025
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 ```
bernt-matthias
added a commit
to bernt-matthias/multi-package-containers
that referenced
this pull request
Jan 26, 2025
can not be built due to strict repo priority which may be fixed in galaxyproject/galaxy#19425
bernt-matthias
added a commit
to bernt-matthias/multi-package-containers
that referenced
this pull request
Jan 26, 2025
cant be built at the moment due to strict repo priority might be possible with galaxyproject/galaxy#19425
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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