[Resending because GMail keeps mangling my email address…]

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

On Apr 3, 2016, at 5:05 AM, Björn Grüning <bjoern.gruening@gmail.com> wrote:

Hi Keith,


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
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