"--net None" option in Galaxy (Docker)
Dear Galaxy team, I'm Jocelyn Brayet, I’m a bioinformatician of Institut Curie (France). I work with Alban Lermine on Galaxy tools development. I currently create tools in Docker for the Galaxy Tool Shed. But, when Galaxy runs Docker, it adds the "—net None" option. The issue is that my tools require annotation files that are downloaded when the job is running (only if the annotation file is not yet available). With "—net None" option I cannot download these annotation files in a Docker. I would like to know if there is a way to switch off this "--net None" option, for instance through the galaxy.ini file ? If so, the user would have the choice to allow Docker to download these files. Many thanks for your feedbacks Best regards Jocelyn
Hi Jocelyn, are you referring to the Docker --net option? https://docs.docker.com/engine/userguide/networking/dockernetworks/ If so you can change the --net option during container startup. For example with docker run --net=host -p 8080:80 bgruening/galaxy-stable I'm wondering if there is not an other issue in your configuration because Galaxy in Docker can connect to the internet without problems. Indeed all our flavours rely on the fact that you can install tools from the ToolShed. Docker containers can have problems with pause and resume on Notebooks, so maybe a restart of your container fixes it? Thanks for using Galaxy! Bjoern On 18.12.2015 13:59, Brayet Jocelyn wrote:
Dear Galaxy team,
I'm Jocelyn Brayet, I’m a bioinformatician of Institut Curie (France). I work with Alban Lermine on Galaxy tools development.
I currently create tools in Docker for the Galaxy Tool Shed. But, when Galaxy runs Docker, it adds the "—net None" option. The issue is that my tools require annotation files that are downloaded when the job is running (only if the annotation file is not yet available). With "—net None" option I cannot download these annotation files in a Docker.
I would like to know if there is a way to switch off this "--net None" option, for instance through the galaxy.ini file ? If so, the user would have the choice to allow Docker to download these files.
Many thanks for your feedbacks Best regards
Jocelyn
Hi; I think I started a thread on a similar issue on this list. The answer was to configure properly config/job_conf.xml, adding the docker runner and the docker_net param within it to "bridge": <?xml version="1.0"?> <!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). --> <job_conf> <plugins> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> </plugins> <handlers> <handler id="main"/> </handlers> <destinations default="docker_local"> <destination id="local" runner="local"/> <destination id="docker_local" runner="local"> <param id="docker_enabled">true</param> <param id="docker_memory">6G</param> <param id="docker_sudo">false</param> <param id="docker_net">bridge</param> </destination> </destinations> </job_conf> Cheers PS: my docker tool: https://github.com/mikel-egana-aranguren/SADI-Docker-Galaxy 2015-12-18 14:07 GMT+01:00 Bjoern Gruening <bjoern.gruening@gmail.com>:
Hi Jocelyn,
are you referring to the Docker --net option?
https://docs.docker.com/engine/userguide/networking/dockernetworks/
If so you can change the --net option during container startup. For example with
docker run --net=host -p 8080:80 bgruening/galaxy-stable
I'm wondering if there is not an other issue in your configuration because Galaxy in Docker can connect to the internet without problems. Indeed all our flavours rely on the fact that you can install tools from the ToolShed.
Docker containers can have problems with pause and resume on Notebooks, so maybe a restart of your container fixes it?
Thanks for using Galaxy! Bjoern
On 18.12.2015 13:59, Brayet Jocelyn wrote:
Dear Galaxy team,
I'm Jocelyn Brayet, I’m a bioinformatician of Institut Curie (France). I work with Alban Lermine on Galaxy tools development.
I currently create tools in Docker for the Galaxy Tool Shed. But, when Galaxy runs Docker, it adds the "—net None" option. The issue is that my tools require annotation files that are downloaded when the job is running (only if the annotation file is not yet available). With "—net None" option I cannot download these annotation files in a Docker.
I would like to know if there is a way to switch off this "--net None" option, for instance through the galaxy.ini file ? If so, the user would have the choice to allow Docker to download these files.
Many thanks for your feedbacks Best regards
Jocelyn
___________________________________________________________ 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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-- Mikel Egaña Aranguren, Ph.D. http://mikeleganaaranguren.com
Hi Bjoern and Mikel, Thanks you very much for your feedbacks ! I have corrected my job_conf.xml and it's ok. Thanks Have a nice week end, Jocelyn ________________________________ De : Mikel Egaña Aranguren [mikel.egana.aranguren@gmail.com] Envoyé : vendredi 18 décembre 2015 14:21 À : Bjoern Gruening Cc : Brayet Jocelyn; galaxy-dev@lists.galaxyproject.org; Servant Nicolas; Lermine Alban Objet : Re: [galaxy-dev] "--net None" option in Galaxy (Docker) Hi; I think I started a thread on a similar issue on this list. The answer was to configure properly config/job_conf.xml, adding the docker runner and the docker_net param within it to "bridge": <?xml version="1.0"?> <!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). --> <job_conf> <plugins> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> </plugins> <handlers> <handler id="main"/> </handlers> <destinations default="docker_local"> <destination id="local" runner="local"/> <destination id="docker_local" runner="local"> <param id="docker_enabled">true</param> <param id="docker_memory">6G</param> <param id="docker_sudo">false</param> <param id="docker_net">bridge</param> </destination> </destinations> </job_conf> Cheers PS: my docker tool:https://github.com/mikel-egana-aranguren/SADI-Docker-Galaxy 2015-12-18 14:07 GMT+01:00 Bjoern Gruening <bjoern.gruening@gmail.com<mailto:bjoern.gruening@gmail.com>>: Hi Jocelyn, are you referring to the Docker --net option? https://docs.docker.com/engine/userguide/networking/dockernetworks/ If so you can change the --net option during container startup. For example with docker run --net=host -p 8080:80 bgruening/galaxy-stable I'm wondering if there is not an other issue in your configuration because Galaxy in Docker can connect to the internet without problems. Indeed all our flavours rely on the fact that you can install tools from the ToolShed. Docker containers can have problems with pause and resume on Notebooks, so maybe a restart of your container fixes it? Thanks for using Galaxy! Bjoern On 18.12.2015 13:59, Brayet Jocelyn wrote: Dear Galaxy team, I'm Jocelyn Brayet, I’m a bioinformatician of Institut Curie (France). I work with Alban Lermine on Galaxy tools development. I currently create tools in Docker for the Galaxy Tool Shed. But, when Galaxy runs Docker, it adds the "—net None" option. The issue is that my tools require annotation files that are downloaded when the job is running (only if the annotation file is not yet available). With "—net None" option I cannot download these annotation files in a Docker. I would like to know if there is a way to switch off this "--net None" option, for instance through the galaxy.ini file ? If so, the user would have the choice to allow Docker to download these files. Many thanks for your feedbacks Best regards Jocelyn ___________________________________________________________ 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/ -- Mikel Egaña Aranguren, Ph.D. http://mikeleganaaranguren.com
participants (3)
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Bjoern Gruening -
Brayet Jocelyn -
Mikel Egaña Aranguren