Subject: bug#37058: Error message with local deployment of Galaxy-k8s

From: "Gao, Jianliang" <[email-masked]>
Date: Fri, 16 Aug 2019 20:17:21 +0000

Hi

I followed https://github.com/phnmnl/phenomenal-h2020/wiki/QuickStart-Installation-for-Local-PhenoMeNal-Workflow with Older Galaxy chart to deploy local galaxy-k8s instance with minikube on Windows 10. The following message came from the logs of my pod. I can't connect to my local instance. Can you please give me some advice to debug it and make it work? Thank you very much.

kubectl logs galaxy-k8s-tr6fc
[ run_galaxy_config.sh ] -- Galaxy sqlite directory created since we are not using postgresql
[ run_galaxy_config.sh ] -- Replaced galaxy ini for the user's injected one
debconf: unable to initialize frontend: Dialog
debconf: (Dialog frontend will not work on a dumb terminal, an emacs shell buffer, or without a controlling terminal.)
debconf: falling back to frontend: Readline
debconf: unable to initialize frontend: Readline
debconf: (This frontend requires a controlling tty.)
debconf: falling back to frontend: Teletype
dpkg-preconfigure: unable to re-open stdin:
 [WARNING]: It is unneccessary to use '{{' in loops, leave variables in loop
expressions bare.

[ run_galaxy_config.sh ] -- Playbook for galaxy config run.
[ run_galaxy_config.sh ] -- Set k8s pull policy to use with Galaxy to IfNotPresent on job_conf.xml
[ run_galaxy_config.sh ] -- Need to set up galaxy database for admin user setup...
/galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:369: SNIMissingWarning: An HTTPS request has been made, but the SNI (Server Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
  SNIMissingWarning
/galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:160: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
  InsecurePlatformWarning
galaxy.tools.deps WARNING 2019-08-16 19:20:48,175 Path './database/dependencies' does not exist, ignoring
galaxy.tools.deps WARNING 2019-08-16 19:20:48,175 Path './database/dependencies' is not directory, ignoring
galaxy.tools.deps.installable WARNING 2019-08-16 19:20:48,190 Conda not installed and auto-installation disabled.
galaxy.tools.deps.installable WARNING 2019-08-16 19:20:48,190 Conda not installed and auto-installation disabled.
tail: unrecognized file system type 0x794c7630 for 'paster.log'. please report this to [email-masked]. reverting to polling

   Best wishes,

Jianliang