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.