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

[Gao, Jianliang]

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 address@hidden. reverting to polling




   Best wishes,

Jianliang