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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