I am running the Docker for Mac (beta) and have a Galaxy, some what customized
via the Dockerfile, but otherwise out of the box. The owner in my mac storage
volume is me and within the docker , root, galaxy, or postgres. I've customized
the welcome.html and base.css.
root@5017ac030db9:/export# ls -l
-rw-r--r-- 1 root root 282334 Jun 20 13:52 base.css
drwxr-xr-x 8 galaxy galaxy 272 Jun 29 17:50 galaxy-central
drwxr-xr-x 3 postgres postgres 102 Jun 1 20:26 postgresql
drwxr-xr-x 4 galaxy galaxy 136 Jun 16 15:46 shed_tools
drwxr-xr-x 3 root root 102 Jun 1 20:26 var
-rw-r--r-- 1 root root 2543 Jun 1 20:28 welcome.html
And on the Mac
dlapoi01$ ls -l
-rw-r--r-- 1 dlapoi01 staff 282334 Jun 20 09:52 base.css
drwxr-xr-x@ 8 dlapoi01 staff 272 Jun 29 13:50 galaxy-central
drwxr-xr-x@ 3 dlapoi01 staff 102 Jun 1 16:26 postgresql
drwxr-xr-x@ 4 dlapoi01 staff 136 Jun 16 11:46 shed_tools
drwxr-xr-x 3 dlapoi01 staff 102 Jun 1 16:26 var
-rw-r--r-- 1 dlapoi01 staff 2543 Jun 1 16:28 welcome.html
So something is at work here. I don't use the —net=HOST but I can connect to
the ports (:8080) from remote systems.
David Lapointe Ph.D.
Sr. Bioinformatics Specialist
Research Technology (RT)
Tufts Technology Services (TTS)
16 Dearborn Road
Somerville MA 02144
on behalf of "Rathert, Philipp, Dr."
Date: Wednesday, June 29, 2016 at 4:23 AM
Subject: [galaxy-dev] Docker for Mac
Dear all I was wondering if anybody has experience running a galaxy production
server using docker for mac. I know it's beta testing at the moment but since
the Virtual machine environment gave us such a hard time preserving and
managing user data etc. I thought I try it anyway...
However, it seems to be not as easy as expected.
after installation of docker I pull the new docker galaxy image with
docker pull quay.io/bgruening/galaxy:16.04
When I start a test container with net=host
docker run -it --net=host quay.io/bgruening/galaxy:16.04)
I am not able to connect to the galaxy web app and get this error:
proftpd: ERROR (abnormal termination)
==> /home/galaxy/logs/slurmd.log <==
[2016-06-29T08:13:41.440] error: Unable to resolve "moby": Unknown host
[2016-06-29T08:13:41.440] error: Unable to establish control machine address
I then tried to use Kinematik and at least I get the web app running. However,
I didn't find the option to change the network settings to net=host
And I have the additional problem that I have to assign ownership rights to the
folders in /export and I get the following error:
chown -R postgres:postgres /postgresql
chown: postgres: illegal group name
I know these are many issues, but maybe one of you has experience with this and
could provide some help.
Thanks a lot,
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