Docker fails to launch galaxy instance.

[thashim]

using command docker run -d -p 8080:80 bgruening/galaxy-stable and accessing port 8080 of the target server gives:

It works!

This is the default web page for this server.

The web server software is running but no content has been added, yet.

Dumping the launch log via docker logs gives

galaxy.tools ERROR 2014-08-20 19:00:36,302 Error reading tool from path: mutation/visualize.xml

Full log at http://privatepaste.com/9373f62213

Perhaps unrelated, but attempting to build the dockerfile locally gives:

ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/galaxy-central/lib/galaxy/util/../../../tool-data/shared/ucsc/builds.txt'
ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/galaxy-central/lib/galaxy/util/../../../tool-data/shared/ucsc/publicbuilds.txt'
ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/galaxy-central/lib/galaxy/util/../../../tool-data/shared/ensembl/builds.txt'
ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/galaxy-central/lib/galaxy/util/../../../tool-data/shared/ncbi/builds.txt'
ERROR: Unable to read builds for site file /galaxy-central/lib/galaxy/util/../../../tool-data/shared/ucsc/ucsc_build_sites.txt

at step Step 60 : RUN service postgresql start && sleep 5 && python create_galaxy_user.py --user [email protected] --password admin --key admin

[thashim]

For what it's worth, none of the errors seem to matter much. I can get this to work by launching using -p 8080:8080 and then running the following sequence of commands

sed -i 's/#host = 127.0.0.1/host=0.0.0.0/g' universe_wsgi.ini
python ./export_user_files.py $PG_DATA_DIR_DEFAULT
service postgresql start
./run.sh

Which suggests its some apache related issue.

[bgruening]

@thashim thanks for your bug report. Can you please provide the docker version you are running?
Also may I ask to start the original docker container and wait for 10 minutes. Under some circumstances Galaxy needs ages to start. I have only seen this in my test environment and never in the docker container, but who knows.

It is very strange that you are seeing the Apache welcome page. There should be a redirect to 8080 and you should see a 'not available' page. So I'm not sure why you are seeing this. Ah this reminds me... are you running it under OS-X?

[thashim]

Docker info gives

Containers: 57
Images: 860
Storage Driver: aufs
 Root Dir: /scratch/docker/aufs
 Dirs: 975
Execution Driver: native-0.2
Kernel Version: 3.13.0-32-generic
Username: thashim
Registry: [https://index.docker.io/v1/]
WARNING: No swap limit support

Waiting 10 mins does not seem to help and we're running this under ubuntu 14.04

[thashim]

If we ssh tunnel port 8080 so that localhost:8080 binds to server:8080, then viewing at localhost:8080 works.

However, even setting host = 0.0.0.0 does not allow the docker container to serve content to non-local addresses. From remote, we still get the same apache page.

[matted-zz]

I believe my commit (d857363) in the pull request I just made solves this issue. There's a default virtualenv that wants to serve requests on port 80, instead of proxying to the Galaxy server which is on 8080.

[bgruening]

@thashim I meant the docker version. Are you using 1.0 or docker 1.1? I'm just curious why this is not happen to me and my test instances.

Matt kindly shared a fix to deactivate the apache standard site. Normally this is not needed but it can't hurt, so please can you test the latest image with Matt's fix included?

Galaxy can run on 127.0.0.1 this is usually not a problem and Apache will proxy this and make it available to the outside.

[thashim]

My bad, we are at

Client version: 1.1.1
Client API version: 1.13
Go version (client): go1.2.1
Git commit (client): bd609d2
Server version: 1.1.1
Server API version: 1.13
Go version (server): go1.2.1
Git commit (server): bd609d2

@matted and I share the same set of machines, so his patch is verified to fix my issue.

[bgruening]

@thashim can we close this issue?

[thashim]

Yes, confimed fixed.