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.

> 
>>>> 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.  
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.

> 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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