Question: (Closed) docker galaxy apt-get update & upgrade error
gravatar for machinelearner
17 months ago by
machinelearner10 wrote:

Hi everyone,

We have recently pulled down an image of the docker Galaxy and created a container with it. Some of the tools that we want to install require perl modules such as GD::Graph. The only way that we were able to get these modules installed were by updating and upgrading apt-get first.

apt-get update
apt-get upgrade
apt-get install libgd-perl

Before the upgrade, the application was able to show up fine on the browser. After the update and the upgrade step, we noticed that Galaxy was no longer able to be displayed. None of the log files seem to have any information on what happened as uwsgi, the handlers, and docker logs all say that the application is running. We tried to check iptables but an error message saying that the user was not root was returned. We were the root user when we tried.

Does anybody know how we can get around or fix this problem? Thanks so much.

galaxy docker • 319 views
ADD COMMENTlink modified 17 months ago • written 17 months ago by machinelearner10

This has been temporarily fixed on our end. Explanation for anyone who stumbles on this problem in the future:

Looks like doing a apt-get upgrade and upgrading all the packages in the container will also upgrade nginx packages. This led to a error log report in /var/log/nginx saying that upload_store directive is unknown.

Upgrading everything except the nginx packages allows for installation of other Perl modules.

ADD REPLYlink written 17 months ago by machinelearner10

Sorry for being so late here. Just to give a little bit feedback, we need to fix to a special version of nginx, that ships with a special upload module. Due to the nature of nginx, we need to compile nginx to make this happen and ship everything from a PPA.

ADD REPLYlink written 17 months ago by Bjoern Gruening5.1k

Solved, temporarily

ADD REPLYlink modified 17 months ago • written 17 months ago by machinelearner10
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