Announcement: Galaxy Docker Image 15.03

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Announcement: Galaxy Docker Image 15.03

Björn Grüning-3
Hi all!

We are proud to present you the next release of Galaxy Docker.

https://github.com/bgruening/docker-galaxy-stable
https://registry.hub.docker.com/u/bgruening/galaxy-stable/

A few highlights:

* based on Galaxy 15.03, with all it's new awesome features
* Docker image is now based on Ubuntu 14.04
* move all required Galaxy dependencies to toolshed/requirements
* use Ansible roles to build large parts of the image
* export the supervisord web-interface (port 9002)
* enable Galaxy reports webapp on GALAXY_URL/reports
* enable/disable services like FTP or Galaxy reports during start-up

The IPython integration was also updated and has a few new libraries to
make it more convenient for R users.

A big thanks to John Chilton for his enormous support and constant input.

The following new releases are available:

 * docker pull bgruening/galaxy-stable:latest_2015.01.13
 * docker pull bgruening/galaxy-stable:15.03
 * docker pull bgruening/galaxy-stable (-> currently 15.03)

As usual feedback is more than welcome!

Cheers,
Bjoern
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Re: Announcement: Galaxy Docker Image 15.03

Michael Crusoe


On Wednesday, March 25, 2015, Björn Grüning <[hidden email]> wrote:
Hi all!

We are proud to present you the next release of Galaxy Docker.

https://github.com/bgruening/docker-galaxy-stable
https://registry.hub.docker.com/u/bgruening/galaxy-stable/

A few highlights:

* based on Galaxy 15.03, with all it's new awesome features
* Docker image is now based on Ubuntu 14.04
* move all required Galaxy dependencies to toolshed/requirements 
* use Ansible roles to build large parts of the image

Super cool. How many dependencies are you having to install from source instead of from Debian packages (either official or 3rd party)?

I think Docker has a lot of usefulness for complicated setups; for software packaging I think making proper Debian packages benefits the entire bioinformatics community more. Bonus: you get a collaborative team (like the Debian Med group) to share the burden.

I don't know what people's interest is in packaging tools and other dependencies for Debian but I'd be happy to talk about it informally; give a formal talk; present a poster; and/or host a BoF on the topic at the Galaxy Community Conference in July.
 
-- 
Michael R. Crusoe

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Re: Announcement: Galaxy Docker Image 15.03

Michael Crusoe
In reply to this post by Björn Grüning-3


On Wednesday, March 25, 2015, Björn Grüning <[hidden email]> wrote:
Hi all!

We are proud to present you the next release of Galaxy Docker.

https://github.com/bgruening/docker-galaxy-stable
https://registry.hub.docker.com/u/bgruening/galaxy-stable/

A few highlights:

* based on Galaxy 15.03, with all it's new awesome features
* Docker image is now based on Ubuntu 14.04
* move all required Galaxy dependencies to toolshed/requirements 
* use Ansible roles to build large parts of the image

Super cool. How many dependencies are you having to install from source instead of from Debian packages (either official or 3rd party)?

I think Docker has a lot of usefulness for complicated setups; for software packaging I think making proper Debian packages benefits the entire bioinformatics community more. Bonus: you get a collaborative team (like the Debian Med group) to share the burden.

I don't know what people's interest is in packaging tools and other dependencies for Debian but I'd be happy to talk about it informally; give a formal talk; present a poster; and/or host a BoF on the topic at the Galaxy Community Conference in July.
 
-- 
Michael R. Crusoe

___________________________________________________________
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:
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Re: Announcement: Galaxy Docker Image 15.03

Björn Grüning-3
Hi Michael,

Am 07.04.2015 um 21:46 schrieb Michael Crusoe:

> On Wednesday, March 25, 2015, Björn Grüning <[hidden email]>
> wrote:
>
>> Hi all!
>>
>> We are proud to present you the next release of Galaxy Docker.
>>
>> https://github.com/bgruening/docker-galaxy-stable
>> https://registry.hub.docker.com/u/bgruening/galaxy-stable/
>>
>> A few highlights:
>>
>> * based on Galaxy 15.03, with all it's new awesome features
>> * Docker image is now based on Ubuntu 14.04
>> * move all required Galaxy dependencies to toolshed/requirements
>
> * use Ansible roles to build large parts of the image
>>
>
> Super cool. How many dependencies are you having to install from source
> instead of from Debian packages (either official or 3rd party)?

A few python packages from pypi, npm and a self-build nginx to get some
extensions in that are currently not available in the official build.

> I think Docker has a lot of usefulness for complicated setups; for software
> packaging I think making proper Debian packages benefits the entire
> bioinformatics community more. Bonus: you get a collaborative team (like
> the Debian Med group) to share the burden.

Sure, if you have any ideas what we can package? I don't think we have
much packages that are not from Debian :)

> I don't know what people's interest is in packaging tools and other
> dependencies for Debian but I'd be happy to talk about it informally; give
> a formal talk; present a poster; and/or host a BoF on the topic at the
> Galaxy Community Conference in July.

I think that in general the entire problem of deployment is very
interesting for the Galaxy community and we have a lot of ideas how to
make it better in/with Galaxy. Not sure about Debians role here, as we
are aiming for a reproducible installation of tools over time.

I will organise a BoF at BOSC to talk in a more general way about
deployment w/wo docker, packages, bioboxes, brew, conda, easyinstall and
so on ... would be great if you can join!

Thanks for caring!
Bjoern





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Re: Announcement: Galaxy Docker Image 15.03

Michael Crusoe


On Wed, Apr 15, 2015 at 2:34 PM, Björn Grüning <[hidden email]> wrote:
Hi Michael,

Am 07.04.2015 um 21:46 schrieb Michael Crusoe:
> On Wednesday, March 25, 2015, Björn Grüning <[hidden email]>
> wrote:
>
>> Hi all!
>>
>> We are proud to present you the next release of Galaxy Docker.
>>
>> https://github.com/bgruening/docker-galaxy-stable
>> https://registry.hub.docker.com/u/bgruening/galaxy-stable/
>>
>> A few highlights:
>>
>> * based on Galaxy 15.03, with all it's new awesome features
>> * Docker image is now based on Ubuntu 14.04
>> * move all required Galaxy dependencies to toolshed/requirements
>
> * use Ansible roles to build large parts of the image
>>
>
> Super cool. How many dependencies are you having to install from source
> instead of from Debian packages (either official or 3rd party)?

A few python packages from pypi, npm and a self-build nginx to get some
extensions in that are currently not available in the official build.

Neat. From personal experience I can tell you that packaging PyPI hosted Python code is pretty straightforward. And https://www.npmjs.com/package/npm2debian looks decent on that front.
 

> I think Docker has a lot of usefulness for complicated setups; for software
> packaging I think making proper Debian packages benefits the entire
> bioinformatics community more. Bonus: you get a collaborative team (like
> the Debian Med group) to share the burden.

Sure, if you have any ideas what we can package? I don't think we have
much packages that are not from Debian :)

The above mentioned python packages, npm packages, and that nginx for starters :-)
 

> I don't know what people's interest is in packaging tools and other
> dependencies for Debian but I'd be happy to talk about it informally; give
> a formal talk; present a poster; and/or host a BoF on the topic at the
> Galaxy Community Conference in July.

I think that in general the entire problem of deployment is very
interesting for the Galaxy community and we have a lot of ideas how to
make it better in/with Galaxy. Not sure about Debians role here, as we
are aiming for a reproducible installation of tools over time.

package name + version + hash + http://snapshot.debian.org/ (as needed) = reproducible

 

I will organise a BoF at BOSC to talk in a more general way about
deployment w/wo docker, packages, bioboxes, brew, conda, easyinstall and
so on ... would be great if you can join!

Huzzah, I will be at BOSC & GCC both and will join in.
 

Thanks for caring!

Of course; cheers,

-- 
Michael R. Crusoe 

___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/