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    Nuwan Goonasekera
    @nuwang
    @pcm32 Haven’t tried this yet. Would be great to hear how it goes
    Pablo Moreno
    @pcm32

    Hi @almahmoud, is this still the correct way of importing the helm repo?

    helm repo add galaxy-gvl https://raw.githubusercontent.com/cloudve/helm-charts/master

    thanks!

    Pablo Moreno
    @pcm32
    yeah, seems to work, please ignore me.. had a different glitch before.
    Pablo Moreno
    @pcm32

    Trying a run with an older value of the helm chart (3.4.2) and cvmfs disabled I get some hard coded CVMFS requirements that make the process fail:

    No handlers could be found for logger "__main__"
    Traceback (most recent call last):
      File "/galaxy/server/scripts/galaxy-main", line 299, in <module>
        main()
      File "/galaxy/server/scripts/galaxy-main", line 295, in main
        app_loop(args, log)
      File "/galaxy/server/scripts/galaxy-main", line 142, in app_loop
        attach_to_pools=args.attach_to_pool,
      File "/galaxy/server/scripts/galaxy-main", line 108, in load_galaxy_app
        **kwds
      File "/galaxy/server/lib/galaxy/app.py", line 115, in __init__
        self._configure_tool_data_tables(from_shed_config=False)
      File "/galaxy/server/lib/galaxy/config/__init__.py", line 1077, in _configure_tool_data_tables
        config_filename=self.config.tool_data_table_config_path)
      File "/galaxy/server/lib/galaxy/tools/data/__init__.py", line 80, in __init__
        self.load_from_config_file(single_config_filename, self.tool_data_path, from_shed_config=False)
      File "/galaxy/server/lib/galaxy/tools/data/__init__.py", line 117, in load_from_config_file
        tree = util.parse_xml(filename)
      File "/galaxy/server/lib/galaxy/util/__init__.py", line 236, in parse_xml
        root = tree.parse(fname, parser=ElementTree.XMLParser(target=DoctypeSafeCallbackTarget()))
      File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 647, in parse
        source = open(source, "rb")
    IOError: [Errno 2] No such file or directory: '/cvmfs/main.galaxyproject.org/config/shed_tool_data_table_conf.xml'

    This is against a fixed container tag for that particular timepoint of the helm chart. So we should check that CVMFS disabled is actually not letting slip any env vars or so on...

    Pablo Moreno
    @pcm32
    mmm… this is affecting all releases of the helm chart marked for 20.01
    Pablo Moreno
    @pcm32
    Ok, the default galaxy.yml added in the config map has (or had back then) a few CVMFs paths that get added even when CVMFS is disabled or they are hard coded there:
    galaxy.yml:
    ----
    galaxy:
      admin_users: you-email-user@your-email-domain.edu,other-admin@email.co.uk
      build_sites_config_file: /galaxy/server/config/build_sites.yml
      builds_file_path: '/cvmfs/data.galaxyproject.org/managed/location/builds.txt'
    there are a few of them… will open an issue.
    Kiran Telukunta
    @telukir_gitlab
    Trying to make ansible script for installing helm over minikube this community.general.helm fails which helm is better on minikube for galaxy in ansible?
    Pablo Moreno
    @pcm32
    @nuwang @almahmoud do you know if there is a new container that doesn’t suffer from galaxyproject/galaxy-helm#160
    People trying to work on the hackathon are suffering from this...
    We still have the job container failing with:
    Exception: Problem parsing the XML in file /galaxy/server/config/job_conf.xml, please correct the indicated portion of the file and restart Galaxy. '>=' not supported between instances of 'NoneType' and ‘tuple’
    Nuwan Goonasekera
    @nuwang
    @pcm32 We were plan on building the latest container. We'll build and push a 20.09 image
    Pablo Moreno
    @pcm32
    Where is the dockefile on github for https://hub.docker.com/r/galaxy/galaxy-k8s/tags ? We could try rebuilding the image ourselves, but the dockerhub entry
    Could we have first a working 20.05 before moving to 20.09?
    Also, how do we go from points in https://github.com/galaxyproject/galaxy-helm to what gets packaged and deposited in https://github.com/CloudVE/helm-charts/tree/master/charts for that repo? I remember that Alex had a CI for this, but I don’t see the links to tags or something else on that repo.
    Dannon
    @dannon
    The prerelease 20.09 images there are ones I built from galaxy-docker-k8s
    The magic in CI has to do with the tags -- I don't know where it actually lives though.
    (so, the tags on the PRs in galaxykubeman-helm)
    I have also requested this be much more transparent, it's just magic without more details pushed back to PRs, etc.
    Pablo Moreno
    @pcm32
    Those tags don’t seem to have relation to the deposited packaged charts...
    image.png
    Dannon
    @dannon
    Sorry, poor choice of word -- github labels.
    I assume the other ones work the same, but my familiarity is with the ones here: https://github.com/galaxyproject/galaxykubeman-helm/pulls?q=is%3Apr+is%3Aclosed
    So, 'patch' 'feature', etc. The github CI is here, but I haven't dug through it to see what it'd take to push back information to PRs: https://github.com/galaxyproject/galaxykubeman-helm/tree/master/.github/scripts
    I'd want to see a response like "This has been published to <blah> as <version>", etc.
    Pablo Moreno
    @pcm32
    Thanks Dannon. Wasn’t aware of galaxykubeman-helm.
    Dannon
    @dannon
    Yeah, galaxyproject/galaxy-helm#142 is the PR that added the same packaging approach to galaxy-helm and it has a little description there.
    Pablo Moreno
    @pcm32
    Thanks! building the container now from galaxy-docker-k8s
    Nuwan Goonasekera
    @nuwang
    @pcm32 Did you get it working? My container build failed because I ran out of disk
    did a clean up and doing a fresh rnu
    Pablo Moreno
    @pcm32
    yes, it is working now with the image I built
    maybe someone can push it back under the galaxy user?
    I appended the initial part of the hash of the galaxy-docker-k8s repo I used (previous commit to the move to 20.09.
    Nuwan Goonasekera
    @nuwang
    ok… Thanks
    Pablo Moreno
    @pcm32
    I tried testing on the galaxy-helm repo, but seems stuck in starting the actual travis run. That repo should be moved to travis-ci.com from current travis-ci.org, but I don’t have the privileges. But I know that the image works as I tested in one of the biohackathon VMs.
    Enis Afgan
    @afgane
    @pcm32 we migrated galaxy-helm to travis-ci.com so at least at the side of org-wide settings, things should be ok. I’m not sure how to make the open PRs switch to .com though, if anyone has advice.
    Pablo Moreno
    @pcm32
    Thanks @afgane ! Yeah, that is tricky, I have done it in the past but don’t remember exactly how. The test seemed to have gone through now though.
    Pablo Moreno
    @pcm32
    Apparently travis is switching to a credit limited setup for free tiers… maybe time to move from there.
    Dannon
    @dannon
    I thought it was free for open source still?
    Pablo Moreno
    @pcm32
    So all our repos (at Expression Atlas) are open source, yet we got:
    Builds have been temporarily disabled for private and public repositories due to a negative credit balance. Please go to the Plan page to replenish your credit balance.
    image.png
    I mention this here since galaxy-helm repo has its CI partly on travis
    Pablo Moreno
    @pcm32
    Dannon
    @dannon
    Ouch. Bad timing for us to move to .com
    I do see:
    We will be offering an allotment of OSS minutes that will be reviewed and allocated on a case by case basis. Should you want to apply for these credits please open a request with Travis CI support stating that you’d like to be considered for the OSS allotment. Please include:
    
        Your account name and VCS provider (like travis-ci.com/github/[your account name] )
        How many credits (build minutes) you’d like to request (should your run out of credits again you can repeat the process to request more or discuss a renewable amount)
    So if anyone has a contact there, we can leverage that, or I (or someone else) can open a support request.
    Pablo Moreno
    @pcm32
    Yes, I just did that for our EBI repos, maybe better if someone else says pretty please from the Galaxy side.
    Apparently they were getting a lot of bitcoin mining and related stuff.
    Dannon
    @dannon
    Ok, I'll send an email. JBrowse folks just had all their builds fail for the same reason, heh.