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
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.
On Mon, Nov 5, 2012 at 5:53 AM, Franco Caramia franco.caramia@petermac.org wrote:
Hi list,
I’m 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
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
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.
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:
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
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:
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
galaxy-dev@lists.galaxyproject.org
-
Franco Caramia -
Joachim Jacob -
Peter Cock