Hi, I am on the way to set up a Docker container on win 10. My problem is that I do not often work on win 10. My idea is to set up a galaxy which can be uses once in a while if needed and will be shutdown or not started if not needed: So I am interested in exporting all datasets including the database. In addition I would like to install tools from the toolshed which will be kept after restarting the docker. So ware I did the following: docker run -d -p 8080:80 -v E:\galaxy_storage\:/export/ bgruening/galaxy-stable its running but there are no files appearing at E:\galaxy_storage\ is it also possible to modify the galaxy.ini? or to ssh to the docker container? Thanks in advance Jochen
Hi Jochen try starting docker with: docker run -i -t -p 8080:80 -v E:\galaxy_storage\:/export/ bgruening/galaxy-stable /bin/bash This will provide an interactive session. You can then start Galaxy (and other stuff like the required PostgreSQL server) with startup > log 2>&1 & and have access to the container. with regard to using the '-v' option: are you using the native docker for Windows or are you using the docker tool box? Regards, Hans-Rudolf On 08/30/2016 10:07 PM, Jochen Bick wrote:
Hi,
I am on the way to set up a Docker container on win 10. My problem is that I do not often work on win 10. My idea is to set up a galaxy which can be uses once in a while if needed and will be shutdown or not started if not needed: So I am interested in exporting all datasets including the database. In addition I would like to install tools from the toolshed which will be kept after restarting the docker.
So ware I did the following: docker run -d -p 8080:80 -v E:\galaxy_storage\:/export/ bgruening/galaxy-stable
its running but there are no files appearing at E:\galaxy_storage\
is it also possible to modify the galaxy.ini?
or to ssh to the docker container?
Thanks in advance Jochen ___________________________________________________________ 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 Hans-Rudolf, thanks for the quick reply.
docker run -i -t -p 8080:80 -v E:\galaxy_storage\:/export/ bgruening/galaxy-stable /bin/bash
this looks really nice. Is it possible to modify galaxy files in the interactive session or will it all be reseted after closing the session?
This will provide an interactive session. You can then start Galaxy (and other stuff like the required PostgreSQL server) with
startup > log 2>&1 &
the startup takes quite a long time and also shows a lot of errors like: could not connect to server: Connection refused Is the server running on host "localhost" (127.0.0.1) and accepting tcp/ip connections on port 5432? and its not running.
and have access to the container.
with regard to using the '-v' option: are you using the native docker for Windows or are you using the docker tool box?
I'm using native docker for Windows. is there any benefit using docker tool box? Best Jochen
Hi Jochen I would definitively go for the native docker for Windows and not using docker tool box. Though, this is based on my experience using native docker for Mac versus docker tool box. Maybe someone else on the list has experience with running Bjoern's docker images on windows? Yes, once you get the '-v' option running, it will be possible to modify galaxy files and keep the changes. Hans-Rudolf On 08/31/2016 01:56 PM, Jochen Bick wrote:
Hi Hans-Rudolf,
thanks for the quick reply.
docker run -i -t -p 8080:80 -v E:\galaxy_storage\:/export/ bgruening/galaxy-stable /bin/bash
this looks really nice. Is it possible to modify galaxy files in the interactive session or will it all be reseted after closing the session?
This will provide an interactive session. You can then start Galaxy (and other stuff like the required PostgreSQL server) with
startup > log 2>&1 &
the startup takes quite a long time and also shows a lot of errors like: could not connect to server: Connection refused Is the server running on host "localhost" (127.0.0.1) and accepting tcp/ip connections on port 5432?
and its not running.
and have access to the container.
with regard to using the '-v' option: are you using the native docker for Windows or are you using the docker tool box?
I'm using native docker for Windows. is there any benefit using docker tool box?
Best Jochen
Hi Hans-Rudolf, here is my progress: If I use Kitematic and download galaxy-stable I can run it and tools can be installed including dataset are also not lost after shutdown. I haven't found the path for my files and I would like to modify also the galaxy.ini. The export path is set to c:/user/documents/kitematic/export but there are no files? On commandline (powershell) it is not possible to get it running. Somehow I get many errors like I told you before and the galaxy instance is never running in my browser. does anyone know where I can find the containers, I mean a path to my containers would be nice? If I run your commands on Linux its of curse working and I can set up everything that I need.... Cheers Jochen On 31.08.2016 16:08, Hans-Rudolf Hotz wrote:
Hi Jochen
I would definitively go for the native docker for Windows and not using docker tool box. Though, this is based on my experience using native docker for Mac versus docker tool box.
Maybe someone else on the list has experience with running Bjoern's docker images on windows?
Yes, once you get the '-v' option running, it will be possible to modify galaxy files and keep the changes.
Hans-Rudolf
On 08/31/2016 01:56 PM, Jochen Bick wrote:
Hi Hans-Rudolf,
thanks for the quick reply.
docker run -i -t -p 8080:80 -v E:\galaxy_storage\:/export/ bgruening/galaxy-stable /bin/bash
this looks really nice. Is it possible to modify galaxy files in the interactive session or will it all be reseted after closing the session?
This will provide an interactive session. You can then start Galaxy (and other stuff like the required PostgreSQL server) with
startup > log 2>&1 &
the startup takes quite a long time and also shows a lot of errors like: could not connect to server: Connection refused Is the server running on host "localhost" (127.0.0.1) and accepting tcp/ip connections on port 5432?
and its not running.
and have access to the container.
with regard to using the '-v' option: are you using the native docker for Windows or are you using the docker tool box?
I'm using native docker for Windows. is there any benefit using docker tool box?
Best Jochen
In addition, this is the error message: *sqlalchemy.exc.OperationalError: (psycopg2.OperationalError) could not connect to server: Connection refused* *Is the server running on host "localhost" (::1) and accepting* *TCP/IP connections on port 5432?* *could not connect to server: Connection refused* *Is the server running on host "localhost" (127.0.0.1) and accepting* *TCP/IP connections on port 5432?* *Removing PID file /home/galaxy/logs/reports.pid* Cheers Jochen On 31.08.2016 16:22, Jochen Bick wrote:
Hi Hans-Rudolf,
here is my progress: If I use Kitematic and download galaxy-stable I can run it and tools can be installed including dataset are also not lost after shutdown. I haven't found the path for my files and I would like to modify also the galaxy.ini. The export path is set to c:/user/documents/kitematic/export but there are no files? On commandline (powershell) it is not possible to get it running. Somehow I get many errors like I told you before and the galaxy instance is never running in my browser.
does anyone know where I can find the containers, I mean a path to my containers would be nice?
If I run your commands on Linux its of curse working and I can set up everything that I need....
Cheers Jochen
On 31.08.2016 16:08, Hans-Rudolf Hotz wrote:
Hi Jochen
I would definitively go for the native docker for Windows and not using docker tool box. Though, this is based on my experience using native docker for Mac versus docker tool box.
Maybe someone else on the list has experience with running Bjoern's docker images on windows?
Yes, once you get the '-v' option running, it will be possible to modify galaxy files and keep the changes.
Hans-Rudolf
On 08/31/2016 01:56 PM, Jochen Bick wrote:
Hi Hans-Rudolf,
thanks for the quick reply.
docker run -i -t -p 8080:80 -v E:\galaxy_storage\:/export/ bgruening/galaxy-stable /bin/bash
this looks really nice. Is it possible to modify galaxy files in the interactive session or will it all be reseted after closing the session?
This will provide an interactive session. You can then start Galaxy (and other stuff like the required PostgreSQL server) with
startup > log 2>&1 &
the startup takes quite a long time and also shows a lot of errors like: could not connect to server: Connection refused Is the server running on host "localhost" (127.0.0.1) and accepting tcp/ip connections on port 5432?
and its not running.
and have access to the container.
with regard to using the '-v' option: are you using the native docker for Windows or are you using the docker tool box?
I'm using native docker for Windows. is there any benefit using docker tool box?
Best Jochen
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/
participants (2)
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Hans-Rudolf Hotz -
Jochen Bick