there is very well maintained Docker image with fully configured Galaxy
- most notably the
recent slide decks for administration training are available here:
Please let us know if you are interested in more.
On Fri, Feb 17, 2017 at 12:14 PM Nir Shachaf <nir.shachaf(a)weizmann.ac.il>
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
Many thanks once more,
*From:* Martin Čech [marten(a)bx.psu.edu]
*Sent:* Thursday, February 09, 2017 6:46 PM
*To:* Nir Shachaf; galaxy-dev(a)bx.psu.edu
*Subject:* Re: [galaxy-dev] regarding tool dependencies
the tool publishing process looks like this: tools for Galaxy are
contributed by developers like you to the Tool Shed
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
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,
On Thu, Feb 9, 2017 at 11:01 AM Nir Shachaf <nir.shachaf(a)weizmann.ac.il>
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:
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,
Plant Sciences Dept.,
Weizmann Inst. of Science,
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