Getting some errors with
planemo shed_lint when checking certain URLs, both in CI and local testing. Example:
Applying linter tool_urls... FAIL .. ERROR: Error '503 Server Error: Service Temporarily Unavailable for url: https://pubs.acs.org/doi/10.1021/ct300849w' accessing https://doi.org/10.1021/ct300849w
When I click through the links work fine (both the full link and the DOI link). Not all the URLs raise errors. Anyone know what's happening here?
The CI run in question is: https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/runs/6485736643?check_suite_focus=true
compare="sim_size"is now discouraged in favour of
assert_contents -> has_size. Assuming I switch, if I am comparing a file that should be of a known size, but different contents, it fails the default
compare="diff"check (which I don't want to run at all) before the
has_sizecheck. I guess I can change the compare type/parameters to something meaningless but passing, but wanted to flag as this doesn't feel like the way it should be
/tmp/tmp5m658hpi/job_working_directory/000/2/tool_script.sh: line 9: run_deepvariant: command not foundAny idea about what could be the problem?
planemo s --galaxy_root ../xx/xxin tools that use docker it shows that error; also when using --biocontainers; however it works fine when using planemo test