Marius van den Beek
Marius van den Beek
@bedroesb I think Andreas' suggestion was to replace https://github.com/galaxyproject/ansible-galaxy-extras/blob/3c6fe3585aa3b82d22f74a1c3eb59afc1a2a49c0/templates/startup_lite.sh.j2#L42 with his suggestion. Did you do this, and if yes, what is the output you're seeing ?
That looks correct, at first glance it looks like some of the tests failed because they couldn't mount the cvmfs shares, and maybe that's why the tests failed ? That...
Old Conda versions were attempting to lock, but that didn't work well and was removed. This is why I would not recommend `conda_auto_install` in production, you'll have the same problem...
Yeah, the proper fix is to activate the conda environment instead of just prepending the path, this should be all that's needed, and that's what run.sh / scripts/common_startup.sh does (https://docs.galaxyproject.org/en/master/admin/framework_dependencies.html#conda).
Oh, interesting. That particular case would be fixed by https://github.com/galaxyproject/galaxy/pull/7889 So what exact docker image are you using now ?
This will be fixed in 19.05, for which the docker image is not yet released.
``` +Linting tool /home/travis/build/bgruening/galaxytools/tools/text_processing/text_processing/cut.xml Applying linter tool_xsd... FAIL .. ERROR: Invalid XML found in file: tmpqjKCNx. Errors [/tmp/tmpqjKCNx:72:0:ERROR:SCHEMASV:SCHEMAV_ELEMENT_CONTENT: Element 'conditional': This element is not expected. Expected is ( action ).]...
the hackish way around this would be to export `GALAXY_CONFIG_NGINX_UPLOAD_STORE=/tmp/nginx_upload_store/`. If `/tmp` is tool small you can export an additional volume to /tmp
> I only see "Failed to communicate with remote job server." That's a job running error, you'll want to check this with Nate, that is not a tool error.
> What's missing: > > * Workflow Reports > * workflow invocations > * a good tutorial on using subworkflows and breaking up workflows to make them modular > *...