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 >>>> > >>>> > ___________________________________________________________ >>>> > 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: >>>> > http://lists.bx.psu.edu/ >>>> > >>>> > To search Galaxy mailing lists use the unified search at: >>>> > http://galaxyproject.org/search/mailinglists/ >>>> ___________________________________________________________ >>>> 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: >>>> http://lists.bx.psu.edu/ >>>> >>>> To search Galaxy mailing lists use the unified search at: >>>> http://galaxyproject.org/search/mailinglists/ >>>> >>> >>> >> >> ___________________________________________________________ >> 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: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > >
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