> Hi Björn,
> Have you pushed the new version to the Docker Hub? When I run the
> galaxy-stable image with the -e BARE=true option I still get a Galaxy
> instance with the default tools.
Yes it is, but you need the :dev version, aka:
docker run -i -t -p 8080:80 bgruening/galaxy-stable:dev
(hope it works, I'm currently not on my PC)
> Also, does this really give me a “bare” Galaxy instance, or just a
> Galaxy instance with an empty tool_conf.xml file?
It only deactivates the tools in tool_conf.xml files. Is this is
problem? These tools do not have any dependencies other than python and
disc space should not be a problem as these are only a bunch of XML files.
The my comments inline.
>> Am 31.03.2016 um 22:17 schrieb Suderman Keith:
>>> Dear Galaxy Team,
>>> Two questions.
>>> 1) Is there a bare-bones version of Galaxy available somewhere?
>>> That is, Galaxy with no tools pre-installed? We are creating
>>> Ansible play books for configuring Docker/Galaxy instances with
>>> our NLP tools installed. Currently we are using a fork of the
>>> Galaxy project with the bio tools removed, but this is less than
>>> ideal when we try to update to new versions of Galaxy.
Can you explain what you delete? I do really support this idea as we are
also developing cheminformatics or imaging flavours.
>>> Alternatively, does anyone have an automated process to delete
>>> unwanted tools that we could run immediately after cloning the
>>> main Galaxy repo?
I don't think so you are pioneering here! But I think the gain of this
step is currently not much, isn't it? What are your concerns?
Disc-space? As a fist shoot I would try to hide genomic-specifc stuff
from users. In a long run we can talk about this with the Galaxy team,
isn't it. I know there is already a consensus of getting tools into the
TS and have as less as possible tools in Galaxy by default.
If you look 3 years back, Galaxy was full of tools, nowadays it's more
or less text manipulation tools without dependencies. So plain XML files
with a few scripts.
>>> 2) Is is possible to either a) modify the existing upload tool,
>>> or b) implement a new upload tool? Several options in the upload
>>> tool do not make sense in our domain (e.g. selecting a genome)
>>> and we would also like to do some post-processing to files after
>>> they have been uploaded. I've looked at the code for the
>>> existing upload tool and it seems quite tightly coupled to the
>>> Galaxy code base.
Yes it is, actually you need to have the upload tool, otherwise many
things do not work.
I would like to go with a)!
That is put big #if #else conditions in the JS and Galaxy code to
display genomic-specific content ... we could have a galaxy.ini config
to trigger this #if.
I do think we have a good chance to get this accepted.
Second step, and this will take for careful thoughts, is a plugin
mechanism for post-upload modifications.
The currently upload tool has some kind of these functionality, for
example the "Space-To-Tab" converter. Ideally exposing tools (even from
>>> I was hoping the "Downgrade upload tool"
>>> thread from a few weeks ago was going to help, but unfortunately
>>> for me (and good for the user) they found a solution that didn't
>>> involve installing a new upload tool.
Let's try to stay as upstream as possible. upload.xml is so tightly
integrated in Galaxy that it is better to get code upstream I assume.
And I know Galaxy devs like the idea of being less genomic centric and
more a general framework. It's just that no one had time for this until
>>> However, could I follow the approach suggested in that thread?
>>> I.E. go back in time and find an old upload.[py | xml] and use
>>> that as a starting point for my own custom upload tool? How far
>>> back in time would I have to go to find an upload.py that was a
>>> standalone tool?
I think this will cause more trouble ... :(
Let me know what you decide I will try to help you as much as I can.
>>> Cheers, Keith
>>> ------------------------------ Research Associate Department of
>>> Computer Science Vassar College Poughkeepsie, NY
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> ------------------------------ Research Associate Department of
> Computer Science Vassar College Poughkeepsie, NY
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