rabbitmq problem with the docker-galaxyp container

[drosofff]

Hi @bgruening

It seems that the docker-galaxyp does not start properly rabbitmq with problem of right access to /usr/local/bin/rabbitmq.sh in the container.
Did I missed something in my docker installation ?

[bgruening]

@drosofff this is new to me. Travis tests are passing to tools can be executed and workflows can be scheduled. Which version are you using, from Dockerhub or quay.io?

[drosofff]

quay.io. I installed Docker CE as specified in https://docs.docker.com/engine/installation/linux/ubuntu/#install-docker and ran the command docker run -d -p 8080:80 -p 8021:21 quay.io/bgruening/galaxy-proteomics as indicated.

I also try to build the image with the Dockerfile, without more success (same rabbitmq error)

[drosofff]

I'll give a shoot using your travis script and let you know

[bgruening]

Are you on Ubuntu?

[drosofff]

yes I am. tested 14.04 and 16.04

[bgruening]

I bet this is the stupid Ubuntu bug with the default storage backend. Can you try to change it to aufs or devicemapper?

[drosofff]

I tried with the travis script.
the make docker_install did not work for me, so I did it manually with apt-get install docker-ce
then make docker_build and make docker_run works ok.

but:

Successfully built 4e458e8ead93
root@instance-1:~/docker-galaxyp# make docker_run
docker run -d -p 8080:80 -p 8021:21 -p 8022:22 \
		--name galaxy_test_container \
		--privileged=true \
		-e GALAXY_CONFIG_ALLOW_USER_DATASET_PURGE=True \
		-e GALAXY_CONFIG_ALLOW_LIBRARY_PATH_PASTE=True \
		-e GALAXY_CONFIG_ENABLE_USER_DELETION=True \
		-e GALAXY_CONFIG_ENABLE_BETA_WORKFLOW_MODULES=True \
		-v /tmp/:/tmp/ \
		galaxy-docker/test
143e6190f8a5d15afee54d04591ede5f472e0f7b93349c66c0802a7764609d57
docker ps
CONTAINER ID        IMAGE                COMMAND              CREATED             STATUS                  PORTS                                                                                           NAMES
143e6190f8a5        galaxy-docker/test   "/usr/bin/startup"   1 second ago        Up Less than a second   443/tcp, 8800/tcp, 9002/tcp, 0.0.0.0:8021->21/tcp, 0.0.0.0:8022->22/tcp, 0.0.0.0:8080->80/tcp   galaxy_test_container
root@instance-1:~/docker-galaxyp# docker logs galaxy_test_container
Enable Galaxy reports authentification
Enable Galaxy Interactive Environments.
Starting postgres
postgresql: started
Checking if database is up and running
root@instance-1:~/docker-galaxyp# docker exec -it galaxy_test_container bash
root@143e6190f8a5:/galaxy-central# supervisorctl status
condor                           STOPPED    Not started
cron                             RUNNING    pid 200, uptime 0:00:17
docker                           STOPPED    Not started
galaxy:galaxy_nodejs_proxy       STOPPED    Not started
galaxy:galaxy_web                RUNNING    pid 160, uptime 0:00:24
galaxy:handler0                  RUNNING    pid 161, uptime 0:00:24
galaxy:handler1                  RUNNING    pid 162, uptime 0:00:24
nginx                            RUNNING    pid 111, uptime 0:00:30
postgresql                       RUNNING    pid 153, uptime 0:00:26
proftpd                          RUNNING    pid 207, uptime 0:00:16
rabbitmq                         FATAL      Exited too quickly (process log may have details)

It may be a docker install problem since I could not reproduce exactly the environment.

[bgruening]

Afaik this is a storage backend problem. You can start the deamon with dockerd --storage-driver string aufs or devicemapper. I hope then it is working. It is known that one of the drivers is broken. The nice thing on this bug is it only occurs in really wired situations and in complex containers with many layers, afaik.

[drosofff]

OK thanks. I shut down my VM to go to bed ;-) I'll see this tomorrow have a good night Christophe Antoniewski ARTbio <http://artbio.fr/> - Tel +33 1 44 2*7 70 05* Drosophila Genetics & Epigenetics <http://drosophile.org/> - Tel +33 1 44 2 *7 34 39*Mobile +33 6 68 60 51 50 https://twitter.com/ARTbio_IBPS https://twitter.com/drosofff 2017-06-15 0:00 GMT+02:00 Björn Grüning <notifications@github.com>:

…

Afaik this is a storage backend problem. You can start the deamon with dockerd --storage-driver string aufs or devicemapper. I hope then it is working. It is known that one of the drivers is broken. The nice thing on this bug is it only occurs in really wired situations and in complex containers with many layers, afaik. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#9 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ALKdGTgTcsPfHXnbyyIpVudcKHshBc7Jks5sEFgSgaJpZM4N5rF6> .

[bgruening]

Sleep well!