unable to install tools from toolshed in custom flavour about docker-galaxy-stable HOT 10 CLOSED

I think this is simply because the on your system postgres needs more time to startup than on Dockerhub or my computer.
During the installation, postgres and Galaxy needs to be started: https://github.com/bgruening/docker-galaxy-stable/blob/dev/galaxy/install_repo_wrapper.sh#L4

Ideally we need to check if postgres is up- and running before starting Galaxy. The downside is it will take slightly longer to install repositories than now.

from docker-galaxy-stable.

So we should probably add someting like

STATUS="$(service ntp status)"   
while [[ ${STATUS} != *"is running"* ]]
do
  STATUS="$(service ntp status)"
done

to the wrapper script and then it should be fixed. Can you add this or should I clone the repo and make a pull request?

Matthias

from docker-galaxy-stable.

I can add this is you like, but can you test it before ... just to make sure my assumption is correct.

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I also get this error. Tried Matthias' solution, but even once the command "service postgresql status" returns status "online" it still fails if you start Galaxy too soon. However, if you wait until the command "psql" no longer returns "FATAL: the database system is starting up", it seems safe to start Galaxy.

Something like:

STATUS=$(psql 2>&1)   
while [[ ${STATUS} =~ "starting up" ]]
do
  STATUS=$(psql 2>&1)
  echo "waiting for database:  $STATUS"
  sleep 1
done

(and switching from sh to bash for this syntax to work btw)

from docker-galaxy-stable.

Hi Saskia,

can you create a PR against the dev branch? I'm a little bit sceptical if we should put this into the new release which can happen every day. But if @matthdsm and you can test this carefully I will get this in. I just can not test it. Never saw this timeout.

from docker-galaxy-stable.

Will do. Yes it used to work for me without this too (couple days ago still) ..not quite sure what changed..

from docker-galaxy-stable.

If we are correct with our assumption, everything that is slowing down the postgres start can be a reason. Watching Galaxy 101 Tutorials on the same computer? ;)

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This fix works for me. A little delay during the startup of postgresql, but everything installs smoothly.
I would propose to integrate it in the new release. Otherwise I'll incorporate it in my "custom flavour" dockerfile.
Thanks for the help Saskia, I hadn't though of monitoring the psql process.

Matthias

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@matthdsm @shiltemann New docker image is ready. Please pull and test the :dev branch.

from docker-galaxy-stable.

I think this is fixed with the latest :dev branch. Thanks @matthdsm and @shiltemann!

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