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:
Starting ProFTP
proftpd: ERROR (abnormal termination)
and
==> /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,
Philipp
On 29 Jun 2016, at 10:23, Rathert, Philipp, Dr. philipp.rathert@ibc.uni-stuttgart.de wrote:
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 think on OSX the user/group is _postgres and it should be
chown -R _postgres:_postgres /export
On 29 Jun 2016, at 10:23, Rathert, Philipp, Dr. philipp.rathert@ibc.uni-stuttgart.de wrote:
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:
Starting ProFTP proftpd: ERROR (abnormal termination)
and
==> /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,
Philipp
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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Hi Ido,
I get no error message, but the command does not change anything. Rights are still assigned to host user and not to postgresql.
Could it be that, since galaxy and other program were running in a docker container, none of these users are known in the actual host environment?
Cheers,
Philipp
-----Original Message----- From: Tamir,Ido [mailto:Ido.Tamir@vbcf.ac.at] Sent: Wednesday, June 29, 2016 12:50 PM To: Rathert, Philipp, Dr. philipp.rathert@ibc.uni-stuttgart.de Cc: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Docker for Mac
On 29 Jun 2016, at 10:23, Rathert, Philipp, Dr. philipp.rathert@ibc.uni-stuttgart.de wrote:
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 think on OSX the user/group is _postgres and it should be
chown -R _postgres:_postgres /export
On 29 Jun 2016, at 10:23, Rathert, Philipp, Dr. philipp.rathert@ibc.uni-stuttgart.de wrote:
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:
Starting ProFTP proftpd: ERROR (abnormal termination)
and
==> /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,
Philipp
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
I don’t know anything about docker - yet. best, ido
On 29 Jun 2016, at 13:02, Philipp Rathert philipp.rathert@ibc.uni-stuttgart.de wrote:
Hi Ido,
I get no error message, but the command does not change anything. Rights are still assigned to host user and not to postgresql.
Could it be that, since galaxy and other program were running in a docker container, none of these users are known in the actual host environment?
Cheers,
Philipp
-----Original Message----- From: Tamir,Ido [mailto:Ido.Tamir@vbcf.ac.at] Sent: Wednesday, June 29, 2016 12:50 PM To: Rathert, Philipp, Dr. philipp.rathert@ibc.uni-stuttgart.de Cc: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Docker for Mac
On 29 Jun 2016, at 10:23, Rathert, Philipp, Dr. philipp.rathert@ibc.uni-stuttgart.de wrote:
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 think on OSX the user/group is _postgres and it should be
chown -R _postgres:_postgres /export
On 29 Jun 2016, at 10:23, Rathert, Philipp, Dr. philipp.rathert@ibc.uni-stuttgart.de wrote:
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:
Starting ProFTP proftpd: ERROR (abnormal termination)
and
==> /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,
Philipp
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
On Jun 29, 2016, at 7:02 AM, Philipp Rathert philipp.rathert@ibc.uni-stuttgart.de wrote:
Hi Ido,
I get no error message, but the command does not change anything. Rights are still assigned to host user and not to postgresql.
Could it be that, since galaxy and other program were running in a docker container, none of these users are known in the actual host environment?
That could very well be, and it is something I was hoping would be fixed in Docker for Mac. My work around in classic Docker is to make sure Galaxy/Postgres use the same GID/UID inside the container as on my host system. However, this requires (as far as I recall) rebuilding the Docker image as this is where UID/GID for Galaxy/Postgres are assigned.
Hope that helps, Keith
Cheers,
Philipp
-----Original Message----- From: Tamir,Ido [mailto:Ido.Tamir@vbcf.ac.at] Sent: Wednesday, June 29, 2016 12:50 PM To: Rathert, Philipp, Dr. philipp.rathert@ibc.uni-stuttgart.de Cc: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Docker for Mac
On 29 Jun 2016, at 10:23, Rathert, Philipp, Dr. philipp.rathert@ibc.uni-stuttgart.de wrote:
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 think on OSX the user/group is _postgres and it should be
chown -R _postgres:_postgres /export
On 29 Jun 2016, at 10:23, Rathert, Philipp, Dr. philipp.rathert@ibc.uni-stuttgart.de wrote:
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:
Starting ProFTP proftpd: ERROR (abnormal termination)
and
==> /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,
Philipp
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
Hi Philipp
I have successfully used "Docker for Mac (beta)” on 10.11.5, but I have always used the traditional location for the image to fetch from: https://index.docker.io/u/bgruening/galaxy-stable/ https://index.docker.io/u/bgruening/galaxy-stable/ (i.e just following the excellent recipes on https://github.com/bgruening/docker-galaxy-stable https://github.com/bgruening/docker-galaxy-stable )
and just by coincidence: last night I tried 'quay.io/bgruening/galaxy:16.04' http://quay.io/bgruening/galaxy:16.04' and it didn’t work, but I haven’t investigated why….
Hans-Rudolf
On 29 Jun 2016, at 10:23, Rathert, Philipp, Dr. philipp.rathert@ibc.uni-stuttgart.de wrote:
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 galaxy:16.04 When I start a test container with net=host docker run -it --net=host quay.io/bgruening/galaxy:16.04 galaxy:16.04) I am not able to connect to the galaxy web app and get this error:
Starting ProFTP proftpd: ERROR (abnormal termination)
and
==> /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 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,
Philipp
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Hans-Rudolph,
This means you use
Docker pull bgruening/galaxy-stable:latest to get the image?
I just noticed that the “latest” image is 6 weeks old and the other only 9 days…
Anyway, I will try if the problems occur with the old one as well.
Did you ever tried to use Docker for mac in a production mode, if yes any idea how to allow acces from other computers in the network?
Cheers,
Philipp
From: Hans-Rudolf Hotz [mailto:hansrudolf.hotz@fmi.ch] Sent: Wednesday, June 29, 2016 3:50 PM To: Rathert, Philipp, Dr. philipp.rathert@ibc.uni-stuttgart.de Cc: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Docker for Mac
Hi Philipp
I have successfully used "Docker for Mac (beta)” on 10.11.5, but I have always used the traditional location for the image to fetch from: https://index.docker.io/u/bgruening/galaxy-stable/ (i.e just following the excellent recipes on https://github.com/bgruening/docker-galaxy-stable )
and just by coincidence: last night I tried ' http://quay.io/bgruening/galaxy:16.04' quay.io/bgruening/galaxy:16.04' and it didn’t work, but I haven’t investigated why….
Hans-Rudolf
On 29 Jun 2016, at 10:23, Rathert, Philipp, Dr. <philipp.rathert@ibc.uni-stuttgart.de mailto:philipp.rathert@ibc.uni-stuttgart.de > wrote:
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/ http://quay.io/bgruening/ galaxy:16.04
When I start a test container with net=host
docker run -it --net=host quay.io/bgruening/ http://quay.io/bgruening/ galaxy:16.04)
I am not able to connect to the galaxy web app and get this error:
Starting ProFTP
proftpd: ERROR (abnormal termination)
and
==> /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 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,
Philipp
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
On 29 Jun 2016, at 15:57, Philipp Rathert philipp.rathert@ibc.uni-stuttgart.de wrote:
Hi Hans-Rudolph, This means you use Docker pull bgruening/galaxy-stable:latest to get the image?
yesy
I just noticed that the “latest” image is 6 weeks old and the other only 9 days…
Anyway, I will try if the problems occur with the old one as well.
Did you ever tried to use Docker for mac in a production mode, if yes any idea how to allow acces from other computers in the network?
only used for training and demonstration purposes so far. haven’t tried to access it over our network, but don’t see a reason why it should not work.
Hans-Rudolf
Cheers,
Philipp
From: Hans-Rudolf Hotz [mailto:hansrudolf.hotz@fmi.ch mailto:hansrudolf.hotz@fmi.ch] Sent: Wednesday, June 29, 2016 3:50 PM To: Rathert, Philipp, Dr. <philipp.rathert@ibc.uni-stuttgart.de mailto:philipp.rathert@ibc.uni-stuttgart.de> Cc: galaxy-dev@lists.galaxyproject.org mailto:galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Docker for Mac
Hi Philipp
I have successfully used "Docker for Mac (beta)” on 10.11.5, but I have always used the traditional location for the image to fetch from: https://index.docker.io/u/bgruening/galaxy-stable/ https://index.docker.io/u/bgruening/galaxy-stable/ (i.e just following the excellent recipes on https://github.com/bgruening/docker-galaxy-stable https://github.com/bgruening/docker-galaxy-stable )
and just by coincidence: last night I tried 'quay.io/bgruening/galaxy:16.04' http://quay.io/bgruening/galaxy:16.04' and it didn’t work, but I haven’t investigated why….
Hans-Rudolf
On 29 Jun 2016, at 10:23, Rathert, Philipp, Dr. <philipp.rathert@ibc.uni-stuttgart.de mailto:philipp.rathert@ibc.uni-stuttgart.de> wrote:
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/ http://quay.io/bgruening/galaxy:16.04 galaxy:16.04
When I start a test container with net=host docker run -it --net=host quay.io/bgruening/ http://quay.io/bgruening/galaxy:16.04 galaxy:16.04)
I am not able to connect to the galaxy web app and get this error:
Starting ProFTP proftpd: ERROR (abnormal termination)
and
==> /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 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,
Philipp
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ http://galaxyproject.org/search/mailinglists/
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 total 281 -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 total 560 -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
Phone: 617-627-5319 Fax: 617-627-3667 http://it.tufts.edu
From: galaxy-dev <galaxy-dev-bounces@lists.galaxyproject.orgmailto:galaxy-dev-bounces@lists.galaxyproject.org> on behalf of "Rathert, Philipp, Dr." <philipp.rathert@ibc.uni-stuttgart.demailto:philipp.rathert@ibc.uni-stuttgart.de> Date: Wednesday, June 29, 2016 at 4:23 AM To: "galaxy-dev@lists.galaxyproject.orgmailto:galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists.galaxyproject.orgmailto:galaxy-dev@lists.galaxyproject.org> 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:
Starting ProFTP
proftpd: ERROR (abnormal termination)
and
==> /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,
Philipp
galaxy-dev@lists.galaxyproject.org
-
Hans-Rudolf Hotz -
Lapointe, David -
Philipp Rathert -
Rathert, Philipp, Dr.
-
Suderman Keith -
Tamir,Ido