Externalizing Galaxy config in docker-galaxy-stable
Hi, My question is to the docker-galaxy-stable community. I would like to use or extend this image with some Galaxy settings externalized. For instance, I would like to define my own GALAXY_UID and GALAXY_HOME environment variables. I have tried the -e setting when I build and run the container, but that doesn't work:
docker run -d -p 8080:80 -p 8021:21 -e "GALAXY_UID=1777" -e "GALAXY_HOME=/home/galaxy/env_test" --name galaxy-env-test bgruening/galaxy-stable ... docker exec -ti galaxy-env-test bash # getent passwd galaxy galaxy:x:1450:1450:Galaxy user:/home/galaxy:
As you can see from above, GALAXY_UID is 1450, as hardcoded in the Dockerfile, and not 1777, as I've specified. Same goes for the home directory. Is there any other way that I can set those variables? If not, what would be the best way to proceed, since, ideally, I would like to extend the galaxy-stable Docker image, and not change the existing one. Currently, I don't see any other way but to fork https://github.com/bgruening/docker-galaxy-stable and change the Dockerfile to externalize those (and other) variables. I hope I can get better suggestions than this. Cheers, Oksana
Hi Oksana, both variables are used during container build to create users and home directories. This does not happen during container startup. They are buildtime variables. All Galaxy ENV vars are runtime variables and do have an impact during startup. Can you tell us more about what you want to do? Thanks, Bjoern
Hi,
My question is to the docker-galaxy-stable community. I would like to use or extend this image with some Galaxy settings externalized. For instance, I would like to define my own GALAXY_UID and GALAXY_HOME environment variables. I have tried the -e setting when I build and run the container, but that doesn't work:
docker run -d -p 8080:80 -p 8021:21 -e "GALAXY_UID=1777" -e "GALAXY_HOME=/home/galaxy/env_test" --name galaxy-env-test bgruening/galaxy-stable ... docker exec -ti galaxy-env-test bash # getent passwd galaxy galaxy:x:1450:1450:Galaxy user:/home/galaxy:
As you can see from above, GALAXY_UID is 1450, as hardcoded in the Dockerfile, and not 1777, as I've specified. Same goes for the home directory.
Is there any other way that I can set those variables? If not, what would be the best way to proceed, since, ideally, I would like to extend the galaxy-stable Docker image, and not change the existing one. Currently, I don't see any other way but to fork https://github.com/bgruening/docker-galaxy-stable and change the Dockerfile to externalize those (and other) variables. I hope I can get better suggestions than this.
Cheers, Oksana
___________________________________________________________ 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 Bjorn, Our team is trying to streamline our Galaxy development process, by using your docker container for development, test and production environments. To do that, our sys admin needs to be able to change a few of Galaxy build time variables, like the ones that I've mentioned and probably more, since our production is running on a cluster and its setup will be quite different from the local dev. We wouldn't want to modify the docker image from environment to environment, so a config file, which would allow to set those build variables before a container is built, would be really useful. Are you planning to extend your development to accommodate this need in the near future? Or if there is already a way to do this that I don't see, please let me know. Cheers, Oksana
On Aug 1, 2015, at 1:10 PM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Oksana,
both variables are used during container build to create users and home directories. This does not happen during container startup. They are buildtime variables.
All Galaxy ENV vars are runtime variables and do have an impact during startup.
Can you tell us more about what you want to do? Thanks, Bjoern
Hi,
My question is to the docker-galaxy-stable community. I would like to use or extend this image with some Galaxy settings externalized. For instance, I would like to define my own GALAXY_UID and GALAXY_HOME environment variables. I have tried the -e setting when I build and run the container, but that doesn't work:
docker run -d -p 8080:80 -p 8021:21 -e "GALAXY_UID=1777" -e "GALAXY_HOME=/home/galaxy/env_test" --name galaxy-env-test bgruening/galaxy-stable ... docker exec -ti galaxy-env-test bash # getent passwd galaxy galaxy:x:1450:1450:Galaxy user:/home/galaxy:
As you can see from above, GALAXY_UID is 1450, as hardcoded in the Dockerfile, and not 1777, as I've specified. Same goes for the home directory.
Is there any other way that I can set those variables? If not, what would be the best way to proceed, since, ideally, I would like to extend the galaxy-stable Docker image, and not change the existing one. Currently, I don't see any other way but to fork https://github.com/bgruening/docker-galaxy-stable and change the Dockerfile to externalize those (and other) variables. I hope I can get better suggestions than this.
Cheers, Oksana
___________________________________________________________ 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, I will think about this, but this comes with the price of doing much of the internal stuff during startup, which also have it's downsides. Can you tell me what your admin wants to do, maybe we find a solution without changing the build-time variables? For example we can talk to schedulers without changing UID/GID ... Thanks for using Galaxy! Bjoern Am 02.08.2015 um 05:19 schrieb Oksana:
Hi Bjorn,
Our team is trying to streamline our Galaxy development process, by using your docker container for development, test and production environments. To do that, our sys admin needs to be able to change a few of Galaxy build time variables, like the ones that I've mentioned and probably more, since our production is running on a cluster and its setup will be quite different from the local dev. We wouldn't want to modify the docker image from environment to environment, so a config file, which would allow to set those build variables before a container is built, would be really useful. Are you planning to extend your development to accommodate this need in the near future? Or if there is already a way to do this that I don't see, please let me know.
Cheers, Oksana
On Aug 1, 2015, at 1:10 PM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Oksana,
both variables are used during container build to create users and home directories. This does not happen during container startup. They are buildtime variables.
All Galaxy ENV vars are runtime variables and do have an impact during startup.
Can you tell us more about what you want to do? Thanks, Bjoern
Hi,
My question is to the docker-galaxy-stable community. I would like to use or extend this image with some Galaxy settings externalized. For instance, I would like to define my own GALAXY_UID and GALAXY_HOME environment variables. I have tried the -e setting when I build and run the container, but that doesn't work:
docker run -d -p 8080:80 -p 8021:21 -e "GALAXY_UID=1777" -e "GALAXY_HOME=/home/galaxy/env_test" --name galaxy-env-test bgruening/galaxy-stable ... docker exec -ti galaxy-env-test bash # getent passwd galaxy galaxy:x:1450:1450:Galaxy user:/home/galaxy:
As you can see from above, GALAXY_UID is 1450, as hardcoded in the Dockerfile, and not 1777, as I've specified. Same goes for the home directory.
Is there any other way that I can set those variables? If not, what would be the best way to proceed, since, ideally, I would like to extend the galaxy-stable Docker image, and not change the existing one. Currently, I don't see any other way but to fork https://github.com/bgruening/docker-galaxy-stable and change the Dockerfile to externalize those (and other) variables. I hope I can get better suggestions than this.
Cheers, Oksana
___________________________________________________________ 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/
We only have one cluster, so we will have both test and production environments running on it. I understand that at a minimum we'd need different Galaxy home dir and UID/GID. This is a proof of concept for us still, so I can't tell you what else we might need to change. I can get hold of our admin on Tuesday and he can clarify if there any other build time variables he needs to change. I'm running with the local dev version and so far it's been great. I just need a local toolshed situation figured out, to be able to install my tools. Thanks for maintaining Galaxy! Will try to contribute once I get more up-to-speed. Cheers, Oksana
On Aug 2, 2015, at 4:23 AM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi,
I will think about this, but this comes with the price of doing much of the internal stuff during startup, which also have it's downsides.
Can you tell me what your admin wants to do, maybe we find a solution without changing the build-time variables? For example we can talk to schedulers without changing UID/GID ...
Thanks for using Galaxy! Bjoern
Am 02.08.2015 um 05:19 schrieb Oksana: Hi Bjorn,
Our team is trying to streamline our Galaxy development process, by using your docker container for development, test and production environments. To do that, our sys admin needs to be able to change a few of Galaxy build time variables, like the ones that I've mentioned and probably more, since our production is running on a cluster and its setup will be quite different from the local dev. We wouldn't want to modify the docker image from environment to environment, so a config file, which would allow to set those build variables before a container is built, would be really useful. Are you planning to extend your development to accommodate this need in the near future? Or if there is already a way to do this that I don't see, please let me know.
Cheers, Oksana
On Aug 1, 2015, at 1:10 PM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Oksana,
both variables are used during container build to create users and home directories. This does not happen during container startup. They are buildtime variables.
All Galaxy ENV vars are runtime variables and do have an impact during startup.
Can you tell us more about what you want to do? Thanks, Bjoern
Hi,
My question is to the docker-galaxy-stable community. I would like to use or extend this image with some Galaxy settings externalized. For instance, I would like to define my own GALAXY_UID and GALAXY_HOME environment variables. I have tried the -e setting when I build and run the container, but that doesn't work:
docker run -d -p 8080:80 -p 8021:21 -e "GALAXY_UID=1777" -e "GALAXY_HOME=/home/galaxy/env_test" --name galaxy-env-test bgruening/galaxy-stable ... docker exec -ti galaxy-env-test bash # getent passwd galaxy galaxy:x:1450:1450:Galaxy user:/home/galaxy:
As you can see from above, GALAXY_UID is 1450, as hardcoded in the Dockerfile, and not 1777, as I've specified. Same goes for the home directory.
Is there any other way that I can set those variables? If not, what would be the best way to proceed, since, ideally, I would like to extend the galaxy-stable Docker image, and not change the existing one. Currently, I don't see any other way but to fork https://github.com/bgruening/docker-galaxy-stable and change the Dockerfile to externalize those (and other) variables. I hope I can get better suggestions than this.
Cheers, Oksana
___________________________________________________________ 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 Sun, Aug 2, 2015 at 4:59 AM, Oksana <okorol@gmail.com> wrote:
We only have one cluster, so we will have both test and production environments running on it. I understand that at a minimum we'd need different Galaxy home dir and UID/GID.
For our local deployment of Galaxy with Docker, which was inspired by a very early version of Björn's docker-galaxy-stable, we use an entrypoint script to remap the Galaxy user's UID and GID inside the container from environment variables GALAXY_UID and GALAXY_GID passed to `docker run`: https://github.com/fredhutchio/docker-galaxy/blob/aa07c5f684d55499a87e77c62a... Just below that, starting at line 42, is an admittedly hacky way of relocating the Galaxy directory hierarchy (exported data and/or code) from its container default location /galaxy to another location specified by the GALAXY_ROOT environment variable. It essentially turns the container into an installer when `--reroot` or `--upgrade` is passed to the entrypoint script. `--reroot` copies the container's entire /galaxy hierarchy to $GALAXY_ROOT for initializing an instance from the container. `--upgrade` copies just the container's Galaxy distribution in /galaxy/stable to $GALAXY_ROOT/stable (aka $GALAXY_HOME) for upgrading an existing instance from a more recent image. It's definitely nice being able to configure things like this at runtime for e.g. differentiating between test and production! Would functionality like this be useful/welcome in docker-galaxy-stable? Cheers, Brian -- Brian Claywell | programmer/analyst Matsen Group | http://matsen.fredhutch.org <http://matsen.fhcrc.org/> Fred Hutchinson Cancer Research Center
Hi Brian, thanks for you mail! Very appreciated, please see my comments inline.
We only have one cluster, so we will have both test and production environments running on it. I understand that at a minimum we'd need different Galaxy home dir and UID/GID.
For our local deployment of Galaxy with Docker, which was inspired by a very early version of Björn's docker-galaxy-stable, we use an entrypoint script to remap the Galaxy user's UID and GID inside the container from environment variables GALAXY_UID and GALAXY_GID passed to `docker run`:
Is this really needed. We could do this in the main image as well, but currently I haven't seen a compelling usecase for this. The downside is that we need to do a lot of `chown/chmod` magic during container startup. But I'm totally willing to do so, if this is was the community is needed. Please also see this latest PR: https://github.com/bgruening/docker-galaxy-stable/pull/71
https://github.com/fredhutchio/docker-galaxy/blob/aa07c5f684d55499a87e77c62a...
Just below that, starting at line 42, is an admittedly hacky way of relocating the Galaxy directory hierarchy (exported data and/or code) from its container default location /galaxy to another location specified by the GALAXY_ROOT environment variable. It essentially turns the container into an installer when `--reroot` or `--upgrade` is passed to the entrypoint script. `--reroot` copies the container's entire /galaxy hierarchy to $GALAXY_ROOT for initializing an instance from the container. `--upgrade` copies just the container's Galaxy distribution in /galaxy/stable to $GALAXY_ROOT/stable (aka $GALAXY_HOME) for upgrading an existing instance from a more recent image.
Interesting! At least for easier upgrading we took a slightly different approach, described here: https://github.com/bgruening/docker-galaxy-stable/tree/dev#upgrading-images Also we store nowadays many original config files in /etc/galaxy/ to make the upgrading smoother. I would be interested in your opinion and if these latest developments would solve your use-cases.
It's definitely nice being able to configure things like this at runtime for e.g. differentiating between test and production! Would functionality like this be useful/welcome in docker-galaxy-stable?
I'm all for it, if this is what is needed by the community. I would just like to keep the initial startup magic by default as minimal as possible. Thanks a lot for your comments, Bjoern
Cheers,
Brian
HI Brian, Thanks for sharing your code. We have just discussed your approach as one possibility of solving our problem, but delayed it as it involved too much hacking :). Now that you've done the hacking, we may revisit it. We were also discussing a possibility of creating access groups with Galaxy UID and cluster process ID to get around the permissions problem that Iyad has described. This would involve extra setup outside Galaxy container, but would possibly remove the need to change GID and UID. Will reply when we've solidified and tested our approach. Bjorn, I would second Brian on being able to configure Galaxy for different environments. To us that was the primary reason of going the docker way. We have considered vagrant, since it seemed like a more mature and more flexible technology for running in production, but went with docker, because Galaxy community supports it. I would personally like to be able to change build-time variables at build, since it's more logical, requires less hacks and the build speed is not as important to me when building containers for different environments, since I'm not going to do that often. I.e.I would still have your lightweight way as a default, but allow to change it for those who need it. That said, I would welcome any standardized solution, be it run time or build time. Cheers, Oksana On Wed, Aug 5, 2015 at 4:30 AM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Brian,
thanks for you mail! Very appreciated, please see my comments inline.
We only have one cluster, so we will have both test and production environments running on it. I understand that at a minimum we'd need different Galaxy home dir and UID/GID.
For our local deployment of Galaxy with Docker, which was inspired by a very early version of Björn's docker-galaxy-stable, we use an entrypoint script to remap the Galaxy user's UID and GID inside the container from environment variables GALAXY_UID and GALAXY_GID passed to `docker run`:
Is this really needed. We could do this in the main image as well, but currently I haven't seen a compelling usecase for this. The downside is that we need to do a lot of `chown/chmod` magic during container startup. But I'm totally willing to do so, if this is was the community is needed.
Please also see this latest PR: https://github.com/bgruening/docker-galaxy-stable/pull/71
https://github.com/fredhutchio/docker-galaxy/blob/aa07c5f684d55499a87e77c62a...
Just below that, starting at line 42, is an admittedly hacky way of relocating the Galaxy directory hierarchy (exported data and/or code)
its container default location /galaxy to another location specified by
from the
GALAXY_ROOT environment variable. It essentially turns the container into an installer when `--reroot` or `--upgrade` is passed to the entrypoint script. `--reroot` copies the container's entire /galaxy hierarchy to $GALAXY_ROOT for initializing an instance from the container. `--upgrade` copies just the container's Galaxy distribution in /galaxy/stable to $GALAXY_ROOT/stable (aka $GALAXY_HOME) for upgrading an existing instance from a more recent image.
Interesting! At least for easier upgrading we took a slightly different approach, described here:
https://github.com/bgruening/docker-galaxy-stable/tree/dev#upgrading-images
Also we store nowadays many original config files in /etc/galaxy/ to make the upgrading smoother. I would be interested in your opinion and if these latest developments would solve your use-cases.
It's definitely nice being able to configure things like this at runtime for e.g. differentiating between test and production! Would functionality like this be useful/welcome in docker-galaxy-stable?
I'm all for it, if this is what is needed by the community. I would just like to keep the initial startup magic by default as minimal as possible.
Thanks a lot for your comments, Bjoern
Cheers,
Brian
-- :: Oksana Korol dataquarry.blogspot.ca
Hi Brian, Oksana, let's move this discussion to github and try to get something done for the next+1 release. 15.07/15.08 or what ever it will be is really close so I would like to not rush here. But as soon as we have release this version. We can try to get something in :dev that addresses these needs. What do you think? Can you create an Issue for it? Thanks! Bjoern Am 05.08.2015 um 15:39 schrieb Oksana Korol:
HI Brian,
Thanks for sharing your code. We have just discussed your approach as one possibility of solving our problem, but delayed it as it involved too much hacking :). Now that you've done the hacking, we may revisit it. We were also discussing a possibility of creating access groups with Galaxy UID and cluster process ID to get around the permissions problem that Iyad has described. This would involve extra setup outside Galaxy container, but would possibly remove the need to change GID and UID. Will reply when we've solidified and tested our approach.
Bjorn,
I would second Brian on being able to configure Galaxy for different environments. To us that was the primary reason of going the docker way. We have considered vagrant, since it seemed like a more mature and more flexible technology for running in production, but went with docker, because Galaxy community supports it.
I would personally like to be able to change build-time variables at build, since it's more logical, requires less hacks and the build speed is not as important to me when building containers for different environments, since I'm not going to do that often. I.e.I would still have your lightweight way as a default, but allow to change it for those who need it. That said, I would welcome any standardized solution, be it run time or build time.
Cheers, Oksana
On Wed, Aug 5, 2015 at 4:30 AM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Brian,
thanks for you mail! Very appreciated, please see my comments inline.
We only have one cluster, so we will have both test and production environments running on it. I understand that at a minimum we'd need different Galaxy home dir and UID/GID.
For our local deployment of Galaxy with Docker, which was inspired by a very early version of Björn's docker-galaxy-stable, we use an entrypoint script to remap the Galaxy user's UID and GID inside the container from environment variables GALAXY_UID and GALAXY_GID passed to `docker run`:
Is this really needed. We could do this in the main image as well, but currently I haven't seen a compelling usecase for this. The downside is that we need to do a lot of `chown/chmod` magic during container startup. But I'm totally willing to do so, if this is was the community is needed.
Please also see this latest PR: https://github.com/bgruening/docker-galaxy-stable/pull/71
https://github.com/fredhutchio/docker-galaxy/blob/aa07c5f684d55499a87e77c62a...
Just below that, starting at line 42, is an admittedly hacky way of relocating the Galaxy directory hierarchy (exported data and/or code)
its container default location /galaxy to another location specified by
from the
GALAXY_ROOT environment variable. It essentially turns the container into an installer when `--reroot` or `--upgrade` is passed to the entrypoint script. `--reroot` copies the container's entire /galaxy hierarchy to $GALAXY_ROOT for initializing an instance from the container. `--upgrade` copies just the container's Galaxy distribution in /galaxy/stable to $GALAXY_ROOT/stable (aka $GALAXY_HOME) for upgrading an existing instance from a more recent image.
Interesting! At least for easier upgrading we took a slightly different approach, described here:
https://github.com/bgruening/docker-galaxy-stable/tree/dev#upgrading-images
Also we store nowadays many original config files in /etc/galaxy/ to make the upgrading smoother. I would be interested in your opinion and if these latest developments would solve your use-cases.
It's definitely nice being able to configure things like this at runtime for e.g. differentiating between test and production! Would functionality like this be useful/welcome in docker-galaxy-stable?
I'm all for it, if this is what is needed by the community. I would just like to keep the initial startup magic by default as minimal as possible.
Thanks a lot for your comments, Bjoern
Cheers,
Brian
Created issue #74, with reference to this discussion. Cheers, Oksana On Wed, Aug 5, 2015 at 9:52 AM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Brian, Oksana,
let's move this discussion to github and try to get something done for the next+1 release.
15.07/15.08 or what ever it will be is really close so I would like to not rush here. But as soon as we have release this version. We can try to get something in :dev that addresses these needs.
What do you think? Can you create an Issue for it? Thanks! Bjoern
Am 05.08.2015 um 15:39 schrieb Oksana Korol:
HI Brian,
Thanks for sharing your code. We have just discussed your approach as one possibility of solving our problem, but delayed it as it involved too much hacking :). Now that you've done the hacking, we may revisit it. We were also discussing a possibility of creating access groups with Galaxy UID and cluster process ID to get around the permissions problem that Iyad has described. This would involve extra setup outside Galaxy container, but would possibly remove the need to change GID and UID. Will reply when we've solidified and tested our approach.
Bjorn,
I would second Brian on being able to configure Galaxy for different environments. To us that was the primary reason of going the docker way. We have considered vagrant, since it seemed like a more mature and more flexible technology for running in production, but went with docker, because Galaxy community supports it.
I would personally like to be able to change build-time variables at build, since it's more logical, requires less hacks and the build speed is not as important to me when building containers for different environments, since I'm not going to do that often. I.e.I would still have your lightweight way as a default, but allow to change it for those who need it. That said, I would welcome any standardized solution, be it run time or build time.
Cheers, Oksana
On Wed, Aug 5, 2015 at 4:30 AM, Björn Grüning <bjoern.gruening@gmail.com
wrote:
Hi Brian,
thanks for you mail! Very appreciated, please see my comments inline.
We only have one cluster, so we will have both test and production environments running on it. I understand that at a minimum we'd need different Galaxy home dir and UID/GID.
For our local deployment of Galaxy with Docker, which was inspired by a very early version of Björn's docker-galaxy-stable, we use an entrypoint script to remap the Galaxy user's UID and GID inside the container from environment variables GALAXY_UID and GALAXY_GID passed to `docker run`:
Is this really needed. We could do this in the main image as well, but currently I haven't seen a compelling usecase for this. The downside is that we need to do a lot of `chown/chmod` magic during container startup. But I'm totally willing to do so, if this is was the community is needed.
Please also see this latest PR: https://github.com/bgruening/docker-galaxy-stable/pull/71
https://github.com/fredhutchio/docker-galaxy/blob/aa07c5f684d55499a87e77c62a...
Just below that, starting at line 42, is an admittedly hacky way of relocating the Galaxy directory hierarchy (exported data and/or code)
its container default location /galaxy to another location specified by
from the
GALAXY_ROOT environment variable. It essentially turns the container into an installer when `--reroot` or `--upgrade` is passed to the entrypoint script. `--reroot` copies the container's entire /galaxy hierarchy to $GALAXY_ROOT for initializing an instance from the container. `--upgrade` copies just the container's Galaxy distribution in /galaxy/stable to $GALAXY_ROOT/stable (aka $GALAXY_HOME) for upgrading an existing instance from a more recent image.
Interesting! At least for easier upgrading we took a slightly different approach, described here:
https://github.com/bgruening/docker-galaxy-stable/tree/dev#upgrading-images
Also we store nowadays many original config files in /etc/galaxy/ to make the upgrading smoother. I would be interested in your opinion and if these latest developments would solve your use-cases.
It's definitely nice being able to configure things like this at
runtime
for e.g. differentiating between test and production! Would functionality like this be useful/welcome in docker-galaxy-stable?
I'm all for it, if this is what is needed by the community. I would just like to keep the initial startup magic by default as minimal as possible.
Thanks a lot for your comments, Bjoern
Cheers,
Brian
-- :: Oksana Korol dataquarry.blogspot.ca
Thanks! @Brian please add your ideas and use cases so we can figure out a way how to support this :) Thanks, Bjoern Am 05.08.2015 um 16:26 schrieb Oksana Korol:
Created issue #74, with reference to this discussion.
Cheers, Oksana
On Wed, Aug 5, 2015 at 9:52 AM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Brian, Oksana,
let's move this discussion to github and try to get something done for the next+1 release.
15.07/15.08 or what ever it will be is really close so I would like to not rush here. But as soon as we have release this version. We can try to get something in :dev that addresses these needs.
What do you think? Can you create an Issue for it? Thanks! Bjoern
Am 05.08.2015 um 15:39 schrieb Oksana Korol:
HI Brian,
Thanks for sharing your code. We have just discussed your approach as one possibility of solving our problem, but delayed it as it involved too much hacking :). Now that you've done the hacking, we may revisit it. We were also discussing a possibility of creating access groups with Galaxy UID and cluster process ID to get around the permissions problem that Iyad has described. This would involve extra setup outside Galaxy container, but would possibly remove the need to change GID and UID. Will reply when we've solidified and tested our approach.
Bjorn,
I would second Brian on being able to configure Galaxy for different environments. To us that was the primary reason of going the docker way. We have considered vagrant, since it seemed like a more mature and more flexible technology for running in production, but went with docker, because Galaxy community supports it.
I would personally like to be able to change build-time variables at build, since it's more logical, requires less hacks and the build speed is not as important to me when building containers for different environments, since I'm not going to do that often. I.e.I would still have your lightweight way as a default, but allow to change it for those who need it. That said, I would welcome any standardized solution, be it run time or build time.
Cheers, Oksana
On Wed, Aug 5, 2015 at 4:30 AM, Björn Grüning <bjoern.gruening@gmail.com
wrote:
Hi Brian,
thanks for you mail! Very appreciated, please see my comments inline.
We only have one cluster, so we will have both test and production environments running on it. I understand that at a minimum we'd need different Galaxy home dir and UID/GID.
For our local deployment of Galaxy with Docker, which was inspired by a very early version of Björn's docker-galaxy-stable, we use an entrypoint script to remap the Galaxy user's UID and GID inside the container from environment variables GALAXY_UID and GALAXY_GID passed to `docker run`:
Is this really needed. We could do this in the main image as well, but currently I haven't seen a compelling usecase for this. The downside is that we need to do a lot of `chown/chmod` magic during container startup. But I'm totally willing to do so, if this is was the community is needed.
Please also see this latest PR: https://github.com/bgruening/docker-galaxy-stable/pull/71
https://github.com/fredhutchio/docker-galaxy/blob/aa07c5f684d55499a87e77c62a...
Just below that, starting at line 42, is an admittedly hacky way of relocating the Galaxy directory hierarchy (exported data and/or code)
its container default location /galaxy to another location specified by
from the
GALAXY_ROOT environment variable. It essentially turns the container into an installer when `--reroot` or `--upgrade` is passed to the entrypoint script. `--reroot` copies the container's entire /galaxy hierarchy to $GALAXY_ROOT for initializing an instance from the container. `--upgrade` copies just the container's Galaxy distribution in /galaxy/stable to $GALAXY_ROOT/stable (aka $GALAXY_HOME) for upgrading an existing instance from a more recent image.
Interesting! At least for easier upgrading we took a slightly different approach, described here:
https://github.com/bgruening/docker-galaxy-stable/tree/dev#upgrading-images
Also we store nowadays many original config files in /etc/galaxy/ to make the upgrading smoother. I would be interested in your opinion and if these latest developments would solve your use-cases.
It's definitely nice being able to configure things like this at
runtime
for e.g. differentiating between test and production! Would functionality like this be useful/welcome in docker-galaxy-stable?
I'm all for it, if this is what is needed by the community. I would just like to keep the initial startup magic by default as minimal as possible.
Thanks a lot for your comments, Bjoern
Cheers,
Brian
Hi, I am also thinking in doing something similar. My idea would be to deploy a galaxy docker on demand per project. The docker would have a galaxy installation that would be configured to join a cluster. Most of the computation would actually occur on the cluster. Each project would thus have its isolated galaxy with separate users. I am extending your docker file with all the tools from the toolshed (I know, it will become a large one-size-fits-all installation). If there is any opinion on this approach, it would be appreciated. I am actually thinking in developing a very small GUI to configure the Dockerfile (say with users and cluster configuration) before build/run. Tiago On Sun, 02 Aug 2015 10:23:20 +0200 Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi,
I will think about this, but this comes with the price of doing much of the internal stuff during startup, which also have it's downsides.
Can you tell me what your admin wants to do, maybe we find a solution without changing the build-time variables? For example we can talk to schedulers without changing UID/GID ...
Thanks for using Galaxy! Bjoern
Am 02.08.2015 um 05:19 schrieb Oksana:
Hi Bjorn,
Our team is trying to streamline our Galaxy development process, by using your docker container for development, test and production environments. To do that, our sys admin needs to be able to change a few of Galaxy build time variables, like the ones that I've mentioned and probably more, since our production is running on a cluster and its setup will be quite different from the local dev. We wouldn't want to modify the docker image from environment to environment, so a config file, which would allow to set those build variables before a container is built, would be really useful. Are you planning to extend your development to accommodate this need in the near future? Or if there is already a way to do this that I don't see, please let me know.
Cheers, Oksana
On Aug 1, 2015, at 1:10 PM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Oksana,
both variables are used during container build to create users and home directories. This does not happen during container startup. They are buildtime variables.
All Galaxy ENV vars are runtime variables and do have an impact during startup.
Can you tell us more about what you want to do? Thanks, Bjoern
Hi,
My question is to the docker-galaxy-stable community. I would like to use or extend this image with some Galaxy settings externalized. For instance, I would like to define my own GALAXY_UID and GALAXY_HOME environment variables. I have tried the -e setting when I build and run the container, but that doesn't work:
docker run -d -p 8080:80 -p 8021:21 -e "GALAXY_UID=1777" -e "GALAXY_HOME=/home/galaxy/env_test" --name galaxy-env-test bgruening/galaxy-stable ... docker exec -ti galaxy-env-test bash # getent passwd galaxy galaxy:x:1450:1450:Galaxy user:/home/galaxy:
As you can see from above, GALAXY_UID is 1450, as hardcoded in the Dockerfile, and not 1777, as I've specified. Same goes for the home directory.
Is there any other way that I can set those variables? If not, what would be the best way to proceed, since, ideally, I would like to extend the galaxy-stable Docker image, and not change the existing one. Currently, I don't see any other way but to fork https://github.com/bgruening/docker-galaxy-stable and change the Dockerfile to externalize those (and other) variables. I hope I can get better suggestions than this.
Cheers, Oksana
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Hi Tiago, Am 03.08.2015 um 15:44 schrieb Tiago Rodrigues Antao:
Hi,
I am also thinking in doing something similar.
My idea would be to deploy a galaxy docker on demand per project. The docker would have a galaxy installation that would be configured to join a cluster. Most of the computation would actually occur on the cluster.
!!! I know of a computer centers that are developing an interface where the user can choose a Docker container, based on their needs. So this is definitely possible
Each project would thus have its isolated galaxy with separate users. I am extending your docker file with all the tools from the toolshed (I know, it will become a large one-size-fits-all installation).
I would recommend you Galaxy Flavours. We have a few, for example RNA-Seq, ChIP-seq etc ... join us! :)
If there is any opinion on this approach, it would be appreciated.
I don't think on container that fits all is good for usability, let's create small special ones.
I am actually thinking in developing a very small GUI to configure the Dockerfile (say with users and cluster configuration) before build/run.
Uh nice! Martin Page and Jeroen Galle are currently working on a Galaxy flavour generator: http://wookoouk.github.io/galaxyFlavorGenerator/ Maybe we could exchange ideas here? Thanks for you mail, Bjoern
Tiago
On Sun, 02 Aug 2015 10:23:20 +0200 Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi,
I will think about this, but this comes with the price of doing much of the internal stuff during startup, which also have it's downsides.
Can you tell me what your admin wants to do, maybe we find a solution without changing the build-time variables? For example we can talk to schedulers without changing UID/GID ...
Thanks for using Galaxy! Bjoern
Am 02.08.2015 um 05:19 schrieb Oksana:
Hi Bjorn,
Our team is trying to streamline our Galaxy development process, by using your docker container for development, test and production environments. To do that, our sys admin needs to be able to change a few of Galaxy build time variables, like the ones that I've mentioned and probably more, since our production is running on a cluster and its setup will be quite different from the local dev. We wouldn't want to modify the docker image from environment to environment, so a config file, which would allow to set those build variables before a container is built, would be really useful. Are you planning to extend your development to accommodate this need in the near future? Or if there is already a way to do this that I don't see, please let me know.
Cheers, Oksana
On Aug 1, 2015, at 1:10 PM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Oksana,
both variables are used during container build to create users and home directories. This does not happen during container startup. They are buildtime variables.
All Galaxy ENV vars are runtime variables and do have an impact during startup.
Can you tell us more about what you want to do? Thanks, Bjoern
Hi,
My question is to the docker-galaxy-stable community. I would like to use or extend this image with some Galaxy settings externalized. For instance, I would like to define my own GALAXY_UID and GALAXY_HOME environment variables. I have tried the -e setting when I build and run the container, but that doesn't work:
docker run -d -p 8080:80 -p 8021:21 -e "GALAXY_UID=1777" -e "GALAXY_HOME=/home/galaxy/env_test" --name galaxy-env-test bgruening/galaxy-stable ... docker exec -ti galaxy-env-test bash # getent passwd galaxy galaxy:x:1450:1450:Galaxy user:/home/galaxy:
As you can see from above, GALAXY_UID is 1450, as hardcoded in the Dockerfile, and not 1777, as I've specified. Same goes for the home directory.
Is there any other way that I can set those variables? If not, what would be the best way to proceed, since, ideally, I would like to extend the galaxy-stable Docker image, and not change the existing one. Currently, I don't see any other way but to fork https://github.com/bgruening/docker-galaxy-stable and change the Dockerfile to externalize those (and other) variables. I hope I can get better suggestions than this.
Cheers, Oksana
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On Mon, 03 Aug 2015 17:30:05 +0200 Björn Grüning <bjoern.gruening@gmail.com> wrote:
I would recommend you Galaxy Flavours. We have a few, for example RNA-Seq, ChIP-seq etc ... join us! :)
That was my first port of call, but they lacked quite a few tools. For example the RNA-Seq lacked tophat, cufflinks and cummrbund. I wanted to reuse as much as possible, but that was what made me stop. I am currently using the stable one (docker-galaxy-stable) and advancing from there. But I would prefer to use a "stock" one. Tiago
Am 04.08.2015 um 00:00 schrieb Tiago Rodrigues Antao:
On Mon, 03 Aug 2015 17:30:05 +0200 Björn Grüning <bjoern.gruening@gmail.com> wrote:
I would recommend you Galaxy Flavours. We have a few, for example RNA-Seq, ChIP-seq etc ... join us! :)
That was my first port of call, but they lacked quite a few tools. For example the RNA-Seq lacked tophat, cufflinks and cummrbund. I wanted to reuse as much as possible, but that was what made me stop.
Create a PR! https://github.com/bgruening/docker-recipes/blob/master/galaxy-rna-seq/Docke...
I am currently using the stable one (docker-galaxy-stable) and advancing from there. But I would prefer to use a "stock" one.
If you feel I can move this into it's own repository and out of docker-recipes. PR welcome! HiSat should be also included I guess. I hope to make this flavours community driven, so I really appreciate contributions to it. Ciao, Bjoern
Tiago
Hi Everyone, As a supplement to Oksana's original inquiry, we, at AAFC, couple Galaxy to SGE and possibly a different grid engine in the future for job scheduling. The old-fashioned way of doing that is to unify storage path and UID/GID between the application server and cluster. The galaxy wiki page refers to this as a "shared file system". I suppose we can configure SGE to submit jobs as a specific user but the resultant files would need to be chowned to the user within the cluster and then back to the one inside the container. Is this supported or has been tested? Regards, Iyad Kandalaft Acting Chief Bioinformatician in Biodiversity, STB Agriculture and Agri-Food Canada / Government of Canada Iyad.Kandalaft@Agr.gc.ca / Tel: 613-759-1228 / TTY: 613-773-2600 Bioinformaticien chef de la biodiversite interim, Direction générale des Science et de la technologie Agriculture et Agroalimentaire Canada / Gouvernement du Canada Iyad.Kandalaft@Agr.gc.ca / Tel: 613-759-1228 / TTY: 613-773-2600 -----Original Message----- From: galaxy-dev [mailto:galaxy-dev-bounces@lists.galaxyproject.org] On Behalf Of Björn Grüning Sent: August-04-15 4:42 AM To: Tiago Rodrigues Antao; Björn Grüning Cc: galaxy-dev@lists.bx.psu.edu; Martin Page (TSL); Oksana; Jeroen Galle Subject: Re: [galaxy-dev] Externalizing Galaxy config in docker-galaxy-stable Am 04.08.2015 um 00:00 schrieb Tiago Rodrigues Antao:
On Mon, 03 Aug 2015 17:30:05 +0200 Björn Grüning <bjoern.gruening@gmail.com> wrote:
I would recommend you Galaxy Flavours. We have a few, for example RNA-Seq, ChIP-seq etc ... join us! :)
That was my first port of call, but they lacked quite a few tools. For example the RNA-Seq lacked tophat, cufflinks and cummrbund. I wanted to reuse as much as possible, but that was what made me stop.
Create a PR! https://github.com/bgruening/docker-recipes/blob/master/galaxy-rna-seq/Docke...
I am currently using the stable one (docker-galaxy-stable) and advancing from there. But I would prefer to use a "stock" one.
If you feel I can move this into it's own repository and out of docker-recipes. PR welcome! HiSat should be also included I guess. I hope to make this flavours community driven, so I really appreciate contributions to it. Ciao, Bjoern
Tiago
___________________________________________________________ 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 Iyad, does this part of our documentation help you? https://github.com/bgruening/docker-galaxy-stable/tree/dev#using-an-external... I now at least of one user that is using the Docker Image in a SLURM cluster environment. I don't see a reason why this should not work on SGE or condor as well. Ciao, Bjoern
Hi Everyone,
As a supplement to Oksana's original inquiry, we, at AAFC, couple Galaxy to SGE and possibly a different grid engine in the future for job scheduling. The old-fashioned way of doing that is to unify storage path and UID/GID between the application server and cluster. The galaxy wiki page refers to this as a "shared file system". I suppose we can configure SGE to submit jobs as a specific user but the resultant files would need to be chowned to the user within the cluster and then back to the one inside the container. Is this supported or has been tested?
Regards,
Iyad Kandalaft
Acting Chief Bioinformatician in Biodiversity, STB Agriculture and Agri-Food Canada / Government of Canada Iyad.Kandalaft@Agr.gc.ca / Tel: 613-759-1228 / TTY: 613-773-2600
Bioinformaticien chef de la biodiversite interim, Direction générale des Science et de la technologie Agriculture et Agroalimentaire Canada / Gouvernement du Canada Iyad.Kandalaft@Agr.gc.ca / Tel: 613-759-1228 / TTY: 613-773-2600
-----Original Message----- From: galaxy-dev [mailto:galaxy-dev-bounces@lists.galaxyproject.org] On Behalf Of Björn Grüning Sent: August-04-15 4:42 AM To: Tiago Rodrigues Antao; Björn Grüning Cc: galaxy-dev@lists.bx.psu.edu; Martin Page (TSL); Oksana; Jeroen Galle Subject: Re: [galaxy-dev] Externalizing Galaxy config in docker-galaxy-stable
Am 04.08.2015 um 00:00 schrieb Tiago Rodrigues Antao:
On Mon, 03 Aug 2015 17:30:05 +0200 Björn Grüning <bjoern.gruening@gmail.com> wrote:
I would recommend you Galaxy Flavours. We have a few, for example RNA-Seq, ChIP-seq etc ... join us! :)
That was my first port of call, but they lacked quite a few tools. For example the RNA-Seq lacked tophat, cufflinks and cummrbund. I wanted to reuse as much as possible, but that was what made me stop.
Create a PR! https://github.com/bgruening/docker-recipes/blob/master/galaxy-rna-seq/Docke...
I am currently using the stable one (docker-galaxy-stable) and advancing from there. But I would prefer to use a "stock" one.
If you feel I can move this into it's own repository and out of docker-recipes. PR welcome! HiSat should be also included I guess.
I hope to make this flavours community driven, so I really appreciate contributions to it.
Ciao, Bjoern
Tiago
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On Tue, 4 Aug 2015 17:26:00 +0000 "Kandalaft, Iyad" <Iyad.Kandalaft@AGR.GC.CA> wrote:
As a supplement to Oksana's original inquiry, we, at AAFC, couple Galaxy to SGE and possibly a different grid engine in the future for job scheduling. The old-fashioned way of doing that is to unify storage path and UID/GID between the application server and cluster.
I am starting to warm of the idea of making a small web interface that asks for a few configuration options: 1. type of grid engine 2. desired docker/galaxy flavour (RNA, exome, WGS, ...) 3. ... (e.g. intial admin user and password) and would pull Björn's relevant Dockerfile, patch it and generate a new one, tailored to the need of the user. I think it is impossible to have a set of dockerfiles for all the desired configurations (think analysis flavours times number of cluster types - for example). I will need to implement something like this very soon, and I would not mind to do it in a way that the community could reuse... So comments would be appreciated...
Tiago, Some work is already in progress for that. Please see - http://wookoouk.github.io/galaxyFlavorGenerator/ - https://github.com/galaxyFlavorsGenerators/galaxyFlavorGenerator/ I don't believe it handles configuration of the cluster backend, but I'm sure that would be a good addition to the project. Ciao, Eric 2015-08-05 10:02 GMT-05:00 Tiago Rodrigues Antao <tra@popgen.net>:
On Tue, 4 Aug 2015 17:26:00 +0000 "Kandalaft, Iyad" <Iyad.Kandalaft@AGR.GC.CA> wrote:
As a supplement to Oksana's original inquiry, we, at AAFC, couple Galaxy to SGE and possibly a different grid engine in the future for job scheduling. The old-fashioned way of doing that is to unify storage path and UID/GID between the application server and cluster.
I am starting to warm of the idea of making a small web interface that asks for a few configuration options: 1. type of grid engine 2. desired docker/galaxy flavour (RNA, exome, WGS, ...) 3. ... (e.g. intial admin user and password)
and would pull Björn's relevant Dockerfile, patch it and generate a new one, tailored to the need of the user.
I think it is impossible to have a set of dockerfiles for all the desired configurations (think analysis flavours times number of cluster types - for example).
I will need to implement something like this very soon, and I would not mind to do it in a way that the community could reuse...
So comments would be appreciated... ___________________________________________________________ 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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-- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas A&M University College Station, TX 77843 404-692-2048 esr@tamu.edu
On Wed, 5 Aug 2015 14:10:57 -0500 Eric Rasche <esr@tamu.edu> wrote:
- http://wookoouk.github.io/galaxyFlavorGenerator/ - https://github.com/galaxyFlavorsGenerators/galaxyFlavorGenerator/
The first link works (for Docker), but the second has only a (empty) readme file...
Hi, the first one is the one we are currently working on. It's an interface to create your own Galaxy Docker flavours. Drag & Drop your tools data managers and so on ... click build and either get a Docker Image or a Docker file. But everything is in flux at the moment. So please jump in and contribute your ideas wherever you can! Bjoern Am 06.08.2015 um 13:42 schrieb Tiago Rodrigues Antao:
On Wed, 5 Aug 2015 14:10:57 -0500 Eric Rasche <esr@tamu.edu> wrote:
- http://wookoouk.github.io/galaxyFlavorGenerator/ - https://github.com/galaxyFlavorsGenerators/galaxyFlavorGenerator/
The first link works (for Docker), but the second has only a (empty) readme file... ___________________________________________________________ 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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On Thu, 06 Aug 2015 14:00:02 +0200 Björn Grüning <bjoern.gruening@gmail.com> wrote:
the first one is the one we are currently working on. It's an interface to create your own Galaxy Docker flavours. Drag & Drop your tools data managers and so on ... click build and either get a Docker Image or a Docker file.
But everything is in flux at the moment. So please jump in and contribute your ideas wherever you can!
1. A notion of a bundle. Say for example a RNA-Seq bundle with packages for that kind of analysis (which the user could still add/remove) 2. The ability to define some kind of iteration with a cluster: choose cluster type (slurm, SGE, LSF, ...), for example Tiago
Hi, Am 06.08.2015 um 15:19 schrieb Tiago Rodrigues Antao:
On Thu, 06 Aug 2015 14:00:02 +0200 Björn Grüning <bjoern.gruening@gmail.com> wrote:
the first one is the one we are currently working on. It's an interface to create your own Galaxy Docker flavours. Drag & Drop your tools data managers and so on ... click build and either get a Docker Image or a Docker file.
But everything is in flux at the moment. So please jump in and contribute your ideas wherever you can!
1. A notion of a bundle. Say for example a RNA-Seq bundle with packages for that kind of analysis (which the user could still add/remove)
We call it flavours: https://raw.githubusercontent.com/bgruening/docker-galaxy-stable/master/char... And yes this should be possible.
2. The ability to define some kind of iteration with a cluster: choose cluster type (slurm, SGE, LSF, ...), for example
This could be as easy as changing two files, so yes should be possible! Ciao, Bjoern
Tiago
participants (7)
-
Björn Grüning -
Brian Claywell -
Eric Rasche -
Kandalaft, Iyad -
Oksana -
Oksana Korol
-
Tiago Rodrigues Antao