seqr deployment fails; timeouts. Centos 7.8 #1409
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I have some findings to add:
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Does anyone have a lead on seqr is supposed to run from behind a department proxy and port? That may be the issue here. |
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Thanks for troubleshooting this further, as I wasn't able to reproduce the issue here. Also, we just updated the docker-compose config to work with the latest postgres image. |
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In docker-compose.yml, I was able to progress, by adding proxy statements "https_proxy" and "http.proxy" (for git, as we need to do that for outbound git requests.) Furthermore, I was able to get past the first postgres error, per this reference: docker-library/postgres#681 However, now the step " |
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Hmm.. I'm not seeing this issue with the latest |
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When I run docker-compose logs postgres, it shows: and for docker-compose logs seqr: Do you see the same thing? |
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You can now also see local deployment logs at the bottom of our travis-ci builds - for example (this is building a branch where the postgres port has been changed to 5433 since 5432 conflicts with the travis-ci environment - the branch code is @ |
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Total error output on "docker-compose exec seqr python manage.py createsuperuser" is below. Traceback (most recent call last): |
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If you run If there's no obvious fix, it may be worth restarting from scratch by running and then running through the install steps again. |
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Hello again.
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One thing: I never ran |
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Great. Yeah, don't worry about branches - they aren't relevant. |
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Total output from: |
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Thanks. I see the issue. The seqr error message tells me it's trying to connect to postgres on The postgres hostname in seqr is determined by the Within docker-compose, it's being set to Is there some reason this may be behaving differently in your environment? |
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So at this point, I noticed this log excerpt: Out of curiosity, I ran the In the event that this is working:
# authenticate to your gcloud account so you can download public reference data What is on the other end of that? |
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@hanars can confirm, but I believe that
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I can confirm that there is no issue with that error |
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Thank you for the guidance. I forgot to mention: There is an error on the documentation link: "TemplateDoesNotExist at /admin/doc/" Any thoughts on that? |
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I'm not sure. What command are you running that produces this error? |
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No command; broken link when I try to web browse http://<seqr_presence_IP>/admin/doc/. |
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thats an error on our seqr too, we just ignore it. http://<seqr_presence_IP>/admin should work fine |
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This may be out-of-scope... In the Google Cloud Platform, "Always" Free language: After a 12-month free trial: I was going to try with my own email address. But you are obliged to leave a card number, so I declined. Do you know how one actually can proceed without credit card? |
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Greetings. With a file docker-compose.yml in place, and python 3.8.1 / docker compose in path, I follow these steps:
sudo docker-compose up -d seqr
sudo /usr/local/docker-compose/docker-compose up -d seqr
However, reviewing those logs confirms that the first step never actually finishes, despite the promising output below.
The logs show that all net-related download actions within the docker are timing out. Example:
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.VerifiedHTTPSConnection object at 0x7f0ab3876450>, 'Connection to pypi.org timed out. (connect timeout=15)')': /simple/django/Adding proxy info to a config ( /root/.docker/config.json, reference: https://medium.com/@airman604/getting-docker-to-work-with-a-proxy-server-fadec841194e) will not avail. Everything halts with thingvs like"Container "4e19a6c5f903" is unhealthy."
In addition to the timeouts, I see mention of a non-existent host postgres. I assume that was to have been created within the docker environment:
psycopg2.OperationalError: could not translate host name "postgres" to address: Name or service not knownThe environment is an oVirt VM running Centos 7.8.
Do you have any leads on the conditions needed to get seqr running? We there special firewall exceptions needed outside of docker?
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