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regarding tool dependencies

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regarding tool dependencies

Nir Shachaf
Dear Galaxy-dev team,

As a research scientist in the dept. of Plant Sciences I would like to contribute a tool to the 'Metabolomics' tool-box under Galaxy. The tool is principally written in R, with some dependencies (namely: R>=3.x, and several R packages). Following the documentation in:

https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies

https://wiki.galaxyproject.org/Admin/Config/ToolDependencies

I admit I get confused by the numerous possibilities offered by the framework. My main concern is to be able to link the Galaxy server to tools already installed on my development environment, and NOT to depend on the tools available in the tool-shed repository (as many are not there, and there are specific versions requirements).

Could you kindly direct me to the relevant solution, or a user's-list post, if applicable?

Many thanks in advance,
Nir Shachaf,
Plant Sciences Dept.,
Weizmann Inst. of Science,
Rehovot, Israel.

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Re: regarding tool dependencies

Martin Čech
Hello Nir,

the tool publishing  process looks like this: tools for Galaxy are contributed by developers like you to the Tool Shed https://toolshed.g2.bx.psu.edu/ which serves as an 'appstore' for Galaxies worldwide. Any Galaxy administrator can then instal the tool. Some tools have dependencies, yours seem to depend on R. The recommended way to have Galaxy installed these dependencies for you is to use Conda (list of some available R packages here: https://anaconda.org/r/repo?type=conda). To learn more about Conda please visit https://docs.galaxyproject.org/en/master/admin/conda_faq.html

Alternatively, when you do not care about sharing your tool, and you do not need to track reproducibility you can add any tool to Galaxy locally (add the .xml wrapper and point tool_conf.xml at it and restart Galaxy). When the tool is executed and no dependencies are found Galaxy will look for its executable and if it is on the $PATH it will just use it.

Please let us know if you have more questions.

Thanks for using Galaxy,

Martin


On Thu, Feb 9, 2017 at 11:01 AM Nir Shachaf <[hidden email]> wrote:
Dear Galaxy-dev team,

As a research scientist in the dept. of Plant Sciences I would like to contribute a tool to the 'Metabolomics' tool-box under Galaxy. The tool is principally written in R, with some dependencies (namely: R>=3.x, and several R packages). Following the documentation in:

https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies

https://wiki.galaxyproject.org/Admin/Config/ToolDependencies

I admit I get confused by the numerous possibilities offered by the framework. My main concern is to be able to link the Galaxy server to tools already installed on my development environment, and NOT to depend on the tools available in the tool-shed repository (as many are not there, and there are specific versions requirements).

Could you kindly direct me to the relevant solution, or a user's-list post, if applicable?

Many thanks in advance,
Nir Shachaf,
Plant Sciences Dept.,
Weizmann Inst. of Science,
Rehovot, Israel.
___________________________________________________________
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/

___________________________________________________________
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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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Re: regarding tool dependencies

Martin Čech
Hi Nir,

there is very well maintained Docker image with fully configured Galaxy available here: http://bgruening.github.io/docker-galaxy-stable/

The documentation for Galaxy administration is linked from here: https://new.galaxyproject.org/docs/#administration - most notably the recent slide decks for administration training are available here: https://gvlproject.github.io/dagobah-training/

If you encounter any problems come to chat with us here: https://gitter.im/galaxyproject/Lobby

Please let us know if you are interested in more.

Martin



On Fri, Feb 17, 2017 at 12:14 PM Nir Shachaf <[hidden email]> wrote:
Dear Martin,

I appreciate your detailed reply. On zero order, my tool, along with other existing Galaxy "metabolomics" tools should work in-house, and therefore I can rely on system dependencies, which might mater be resolved through some help from the community.

However, I would like to raise a slightly bigger issue, as at least for me, setting up the Galaxy framework is a very intricate job, evolving editing several configuration files which goes much beyond the setting of package dependencies. In my opinion it would be very useful to have some "quick start recipes", or a predefined VM which can work out of the box, including, e.g. a per-configured demo users' DB and a linked FTP server for uploading files, etc. At least, a tutorial on how to setup such a system on several popular Linux configurations would be greatly appreciated! At the moment, I have abandoned the idea of setting up Galaxy in my lab, due to time-consuming configuration problems... hopefully, we can re-try in the future.

Many thanks once more,
Nir.


From: Martin Čech [[hidden email]]
Sent: Thursday, February 09, 2017 6:46 PM
To: Nir Shachaf; [hidden email]
Subject: Re: [galaxy-dev] regarding tool dependencies

Hello Nir,

the tool publishing  process looks like this: tools for Galaxy are contributed by developers like you to the Tool Shed https://toolshed.g2.bx.psu.edu/ which serves as an 'appstore' for Galaxies worldwide. Any Galaxy administrator can then instal the tool. Some tools have dependencies, yours seem to depend on R. The recommended way to have Galaxy installed these dependencies for you is to use Conda (list of some available R packages here: https://anaconda.org/r/repo?type=conda). To learn more about Conda please visit https://docs.galaxyproject.org/en/master/admin/conda_faq.html

Alternatively, when you do not care about sharing your tool, and you do not need to track reproducibility you can add any tool to Galaxy locally (add the .xml wrapper and point tool_conf.xml at it and restart Galaxy). When the tool is executed and no dependencies are found Galaxy will look for its executable and if it is on the $PATH it will just use it.

Please let us know if you have more questions.

Thanks for using Galaxy,

Martin


On Thu, Feb 9, 2017 at 11:01 AM Nir Shachaf <[hidden email]> wrote:
Dear Galaxy-dev team,

As a research scientist in the dept. of Plant Sciences I would like to contribute a tool to the 'Metabolomics' tool-box under Galaxy. The tool is principally written in R, with some dependencies (namely: R>=3.x, and several R packages). Following the documentation in:

https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies

https://wiki.galaxyproject.org/Admin/Config/ToolDependencies

I admit I get confused by the numerous possibilities offered by the framework. My main concern is to be able to link the Galaxy server to tools already installed on my development environment, and NOT to depend on the tools available in the tool-shed repository (as many are not there, and there are specific versions requirements).

Could you kindly direct me to the relevant solution, or a user's-list post, if applicable?

Many thanks in advance,
Nir Shachaf,
Plant Sciences Dept.,
Weizmann Inst. of Science,
Rehovot, Israel.
___________________________________________________________
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/
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