search

galaxyproteomics / tools-galaxyp

Galaxy Tool Shed repositories maintained and developed by the GalaxyP community
MIT License
34 stars 57 forks source link

update macros.xml and maxquant.xml #700

Closed mthang closed 1 year ago

mthang commented 1 year ago

@bgruening I have updated the macros.xml and maxquant.xml file on the top of the @npinter latest fix. In brief, I updated the version of Maxquant from 1.6.17.0 to 2.0.3.0 , updated the pyyaml version and added the dotnet as part of the requirement section. Everything is looking good now.

Best

bgruening commented 1 year ago

@mthang thanks a lot. Can you please look at the failing tests?

bgruening commented 1 year ago

Its still failing @mthang :(

mthang commented 1 year ago

Hopefully this updated maxquant works @bgruening

bgruening commented 1 year ago

Still fails unfortunately. Are you using planemo test --biocontainers?

mthang commented 1 year ago

@bgruening I just used planemo test --update_test_data --galaxy_root=/path/to/my/local/galaxy_21.05 maxquant.xml . Nothing fancy.

bgruening commented 1 year ago

Have a look at @bernt-matthias comment. You need to adopt the test data properly. And running them in containers as here on CI night also help.

bernt-matthias commented 1 year ago

@mthang: please run tests with:

planemo test --biocontainers --no_dependency_resolution --no_conda_auto_init --galaxy_branch release_23.0 --galaxy_python_version 3.7 --test_timeout 900 --no_cleanup tools/maxquant/

Seemst that for maxquant_mqpar the parameter file needs an update. If updating the separate files in test-data is to much work I can also live with it as long as it survives at least to planemo test rounds. The first test times ou on CI because it needs to much time to build the container. Maybe you can double check if all requirements are needed. Alternatively we can build the container first in the multi-package container repo to make tests run through over here.

bernt-matthias commented 1 year ago

Closing in favor of https://github.com/galaxyproteomics/tools-galaxyp/pull/716