Hi Keith,

Hi Björn,

Yes it is, but you need the :dev version,
DOH, I should have known…

:)

Can you explain what you delete? I do really support this idea as we are
also developing cheminformatics or imaging flavours.
Currently I think I have just removed the datatypes.  I haven’t removed 
anything else as I didn’t know how many, if any, were tightly coupled as the 
upload tool is.

We could think about removing datatypes as well from the BARE Galaxy Docker container, similar to what we have done now for tools, if you like.

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?
Not really concerns, I just would like to remove as much unneeded code as 
possible.  I have removed all (most) of the default datatypes shipped with 
Galaxy as many of the file extensions conflict with extension I want to use.

Mh, but I see a bigger problem here. If you have conflicting extensions, could you not prefix them? I have the small dream of having a university workbench with all tools. So offering your tools as well as genomics and in this case I will have the problems again. Removing genomic datatypes makes sense in your case and I'm happy to work on this. But it would be nice if we could also try to make these tools, datatypes work on every Galaxy instance.

Can we prepend them with 'nltk_'?

  Since the tools are most likely broken without the correct datatypes 
available my feeling is that these tools simply provide added points of failure 
and/or additional attack vectors for hackers.  I have been dealing with some 
brute-force attacks on our Wordpress installation the past few weeks that has 
taught me that any unused code, regardless of how innocuous it seems, simply 
provides avenues of attack.

True, but if you deactivate datatypes the code should not be loaded and with every modification we do that is not tested we increase the attack vector again.

Let me know what you decide and if you like to use the Docker container and I will find time to get rid of datatypes in BARE mode.

Thanks,
Bjoern

Yes it is, actually you need to have the upload tool, otherwise many
things do not work.
I would like to go with a)!
I think you are correct; modifying the current upload tool is the way to go.  A 
plugin mechanism for post-processing uploaded files sounds like a great idea!

Cheers,
Keith

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
the TS)?


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
know.

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,
Bjoern

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

------------------------------
Research Associate
Department of Computer Science
Vassar College
Poughkeepsie, NY


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