GNU bug report logs - #37058
Error message with local deployment of Galaxy-k8s

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: "Gao, Jianliang" <j.gao <at> imperial.ac.uk>
To: "bug-coreutils <at> gnu.org" <bug-coreutils <at> gnu.org>
Subject: Error message with local deployment of Galaxy-k8s
Date: Fri, 16 Aug 2019 20:17:21 +0000

[Message part 1 (text/plain, inline)]

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 bug-coreutils <at> gnu.org. reverting to polling




   Best wishes,

Jianliang

[Message part 2 (text/html, inline)]

Message #8 received at 37058 <at> debbugs.gnu.org (full text, mbox):

From: Assaf Gordon <assafgordon <at> gmail.com>
To: "Gao, Jianliang" <j.gao <at> imperial.ac.uk>, 37058 <at> debbugs.gnu.org
Subject: Re: bug#37058: Error message with local deployment of Galaxy-k8s
Date: Fri, 16 Aug 2019 15:45:33 -0600

tag 37058 notabug
close 37058
stop

Hello,

Two issues are mixed here.

First:

On 2019-08-16 2:17 p.m., Gao, Jianliang wrote:
> 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. 

[...]
> 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
[...]
> dpkg-preconfigure: unable to re-open stdin:
>   [WARNING]: It is unneccessary to use '{{' in loops, leave variables in loop
> expressions bare.
[...]
> 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.

These are issues related your Galaxy setup.

(for other readers: "Galaxy" in this context is a web-based framework 
for bioinformatics analysis, see https://galaxyproject.org/ and 
https://usegalaxy.org ).

Such issues are best asked in their support forums:
   https://galaxyproject.org/support/
   https://help.galaxyproject.org

This includes problems in underlying layers, such as the 'dpkg' errors
above that result from deploying Galaxy VMs or instances or kubernetes 
or containers etc.

> tail: unrecognized file system type 0x794c7630 for 'paster.log'. please report this to bug-coreutils <at> gnu.org. reverting to polling

This warning indeed comes from coreutils program 'tail',
however it is harmless in your situation.
For more details, see here:
  https://www.gnu.org/software/coreutils/filesystems.html

---

A cursory look at the error logs makes it seem like
"bug-coreutils <at> gnu.org" is the place to ask General questions about 
"Galaxy" server (because it is the last thing mentioned),
but that is not the case.
We can only help with coreutils programs (e.g. 'tail').

Please contact the Galaxy team for galaxy-related issues.

Hope this helps.
regards,
 - assaf

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