[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/ <https://lists.galaxyproject.org/>
>>>> 
>>>> To search Galaxy mailing lists use the unified search at:
>>>> http://galaxyproject.org/search/mailinglists/ 
>>>> <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.gruen...@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

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