Yes, primer3 is available as a command line tool, it was just an example, the one I'm actually after is optimus primer.. I'm sure there are several web-tools out there that would be nice to get to Galaxy... Any Ideas?? Regards, Franco On 5/11/12 11:18 PM, "Peter Cock" <p.j.a.cock@googlemail.com> wrote:

On Mon, Nov 5, 2012 at 5:53 AM, Franco Caramia <franco.caramia@petermac.org> wrote:

...

Hi list,

I¹m trying to find documentation or examples on how to wrap web-tools (like primer3, optimus primer) in Galaxy.

Any useful links or examples would be of great help.

Thanks,

Franco

I'm not answering your question, but Primer3 is available as a command line tool, so why do you want to wrap a web-tool version of it?

Also EMBOSS have a command line wrapper providing a conventional Unix API to primer3. There are some EMBOSS wrappers in the Galaxy ToolShed, but I don't see one for primer3 yet.

Regards,

Peter

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On Tue, Nov 6, 2012 at 11:34 PM, Franco Caramia <franco.caramia@petermac.org> wrote:

Yes, primer3 is available as a command line tool, it was just an example, the one I'm actually after is optimus primer.. I'm sure there are several web-tools out there that would be nice to get to Galaxy... Any Ideas??

Galaxy does have some tools which fetch data from an online resource, for example BioMoby, UCSC, etc. Many of these call into another website (i.e. don't have to pass any Galaxy information to the 3rd party) so are not suitable. The "Get Microbial Data" does start with a Galaxy tool interface allowing you to pick options... However, I am not aware of any truly analogous examples to what you want. In your shoes what I would do is write a 'stand alone' command line script which Galaxy can call like any other tool (you write an XML file specifying the inputs, e.g. a FASTA file). Your custom script must then call the 3rd party website, set any options, upload any input files (e.g. a FASTA file of sequences), and then wait for the remote service to finish, download the data, perhaps parse the HTML to reformat it into something more useful like a tabular file - and then finish. You'd need lots of error handling too of course ;) The critical point here is your wrapper script will block - it will keep running (e.g. in a sleep and poll loop) until the remote site finishes or fails, and only then return the results to Galaxy. i.e. From Galaxy's perspective it will be a simple command line which just takes a while to run. If the remote site provides a web API this might not be too hard. If their only interface is intended for human usage, then technically it might not be very easy. If you have to collect results via email it will be even more complicated. Also, check the remote site's terms and conditions, wrapping it in Galaxy may not be permitted. Contact the site owners - they may prefer to release their own binaries with a Galaxy wrapper? Regards, Peter