Would require some adjustment on the server side of the webtool I think: to allow getting data in from URLs and to export the results to a URL (API). On the wiki, you can find this info on how to get data IN into Galaxy: http://wiki.galaxyproject.org/Admin/Internals/Data%20Sources But there is no way to get data out of Galaxy to your webtool I think, and get the results back in a way that Galaxy knows what has been executed. (Perhaps one possible start of a solution: make your dataset public, and send the URL (if on a public Galaxy) to the tool (if it accepts URLs)). Anyway, on a higher level, the purpose of Galaxy is not to communicate with webtools, but providing a front-end to command-line tools and a data tracking and analysis platform. (all of which collides with the integration of webtools IMO) (also like: sometimes you don't even get the source-code behind a scientific webservice). Have a nice wednesday, Joachim Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 11/07/2012 12:34 AM, Franco Caramia 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??
Regards,
Franco
On 5/11/12 11:18 PM, "Peter Cock" <p.j.a.cock@googlemail.com> 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
On Mon, Nov 5, 2012 at 5:53 AM, Franco Caramia <franco.caramia@petermac.org> wrote: 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
This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.
___________________________________________________________ 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: