Sorry, I meant Tool Factory when I wrote Tool Shed in my previous email.

On Tue, Jun 10, 2014 at 5:25 PM, Ross <ross.laza...@gmail.com> wrote:

>
>
> On Tue, Jun 10, 2014 at 7:37 AM, Karthik Gururaj <
> gururaj.kart...@gmail.com> wrote:
>
>> Thanks - will take a look at the Tool Shed and see if there is anything
>> there we can use in safe manner. Else, the old fashioned way of asking
>> users to test out on their tools on a standalone Galaxy system and then
>> requesting the administrator to pull in the relevant XML files.
>>
>
> Sorry this is a bit confusing...
> Just to be quite clear: The Tool Factory is available from the main Tool
> Shed, but Tool Factory =/= Tool Shed !!
>
> The Tool Factory is just another Galaxy tool administrators can use to run
> scripts interactively in Galaxy.
> It installs automatically from the main Tool Shed and optionally generates
> new Galaxy tools from working scripts.
> New generated tools are in a tgz archive ready to be uploaded into Tool
> Shed repositories.
>
> The Tool Shed is a specialised web server that supports version control
> and management of Galaxy tool source code and automated installation into
> Galaxy instances.
> You could run a local Tool Shed and yes, your admins could use it to
> install properly configured user provided tools.
>
> The Tool Factory allows your scripting-capable users of creating new
> Galaxy tools from scripts if they run it as administrators of their own
> laptop/development instances, or your administrators could use it to run
> scripts directly on your private instance and optionally generate new safe
> tools (by uploading the archives to your local tool shed then installing
> those new tools into your local Galaxy) for ordinary users to use in their
> workflows.
>
>
>
>
>>  Thanks,
>> Karthik
>>
>>
>> On Sun, Jun 8, 2014 at 6:25 PM, Ross <ross.laza...@gmail.com> wrote:
>>
>>> Hi, Karthik and John.
>>>
>>> Some details on the tool factory for anyone interested.
>>>
>>> Executive summary: it may be helpful in this context but only for
>>> trusted administrators.
>>>
>>> TL;DR:
>>>
>>> Firstly, it will refuse to run for anyone other than a local Galaxy
>>> administrator. This is because it exposes unrestricted scripting so should
>>> only be installed if you can trust your administrative users not to run "cd
>>> /; rm -rf *". I'd advise installing ONLY on your own private instance and
>>> NEVER on a public Galaxy.
>>>
>>> Secondly, it has two modes of operation - script running and tool
>>> generation.
>>>
>>> When executed without the option to generate a tool archive, it will run
>>> a pasted (perl, python, R, bash) script creating an output in the history.
>>> This history output is re-doable in the usual Galaxy way including allowing
>>> the script to be edited and rerun, so it's possible to (eg) get a script
>>> working interactively - galaxy as an IDE anyone ? :)
>>>
>>> Once a script runs on some test data, the tool factory will optionally
>>> generate a complete tool shed compatible gzip which can be uploaded to any
>>> tool shed as a new or updated repository. The generated tool includes the
>>> supplied test data as a proper Galaxy functional test. Once a tool is in a
>>> toolshed, it is just another Galaxy tool, ready to be installed to any
>>> Galaxy like any other tool - but will require restarting of multiple web
>>> processes as John mentions.
>>>
>>> If the script is safe, the tool is safe - there are no specific security
>>> risks for tool factory generated tools other than the script itself.
>>>
>>> Finally, currently it takes only one input and generates one output
>>> which is a substantial restriction - but of course the generated tool
>>> source code is easy to edit if you need more complex I/O. It has a really
>>> neat option to create a simple but useful HTML display with links and
>>> thumbnails to arbitrary (eg) pdf or other output files from a script - the
>>> tool form includes examples in all 4 scripting languages ready to cut and
>>> paste, including one which generates 50 random images and presents them in
>>> a grid as an HTML page for the user.
>>>
>>> On Mon, Jun 9, 2014 at 10:32 AM, John Chilton <jmchil...@gmail.com>
>>> wrote:
>>>
>>>> Galaxy doesn't really support this use case and it will be major
>>>> effort to get it work this way I suspect. Pieces to look at include:
>>>>
>>>> The Galaxy Tool Factory (it has the ability to create reusable tools
>>>> from scripts):
>>>>
>>>> http://www.ncbi.nlm.nih.gov/pubmed/23024011
>>>>
>>>> You may be able to modify it in such a way that each tool is tagged
>>>> with who created and then use ToolBox filters to limit added tools to
>>>> a given user:
>>>>
>>>> https://wiki.galaxyproject.org/UserDefinedToolboxFilters
>>>>
>>>> I think the latest version of Galaxy has improved support for adding
>>>> tools without requiring restarts (using message queues). I don't know
>>>> if this will automatically work with the tool factory or not.
>>>>
>>>> I suspect fighting Galaxy at every step on this will frustrate you and
>>>> the users - and you are exposing all of your users data to every user
>>>> you give this privilege to. Is this a shared cluster or is dedicated
>>>> to Galaxy? If it is shared - it might be better for advanced users to
>>>> just get importing and exporting data to user directories really well.
>>>> In my previous position at MSI we created a set of tools that allowed
>>>> Galaxy to SCP files as the user to our login nodes (using a SSH key
>>>> scheme) - likewise creating directories user's can upload files can
>>>> enabled power users.
>>>>
>>>> Hopefully this helps,
>>>>
>>>> -John
>>>>
>>>> On Sat, Jun 7, 2014 at 1:12 PM, Karthik Gururaj
>>>> <gururaj.kart...@gmail.com> wrote:
>>>> > Hello,
>>>> >   We have a centralized Galaxy installation for out cluster which can
>>>> be
>>>> > used by many users (backend interfaces with HTCondor to run jobs). Is
>>>> there
>>>> > any way for non-administrator users to import/install their own tools
>>>> so
>>>> > that they may use it in their workflows (under a subsection called
>>>> > "unstable", for example? Ideally, without having to restart the Galaxy
>>>> > daemons whenever a change is made.
>>>> > It would be fine if these tools are not visible to other users till
>>>> the
>>>> > administrator says so.
>>>> > Thanks,
>>>> > Karthik
>>>> >
>>>> > ___________________________________________________________
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>>>
>>>
>>
>> ___________________________________________________________
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>
>
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