[Resending (again) as GMail keeps mangling my email address… sorry for triple posting...]

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
On Apr 4, 2016, at 7:01 PM, Suderman Keith <keithsuderman@gmail.com> wrote:

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



___________________________________________________________
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/


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


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

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