Hi Peter, I have used UGene before: it is a nice tool. I am not sure I have understood your question. The easiest way to integrate your tool in Galaxy, is that your tool can be driven by the command line (no GUI). The tool and parameters should be configured by a tool config file, as you mentioned. The other way around (let UGene use Galaxy tools) is that you use Galaxy's API to submit jobs and return the results. Plenty of documentation can be found on Galaxy's wiki pages! wiki.galaxyproject.org Hope this helps you a bit further, Joachim Jacob. Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 08/05/2013 12:19 PM, Пётр Леонтьев wrote:

Hello, Galaxy team. I am writing you to find out the right way about how can be other bioinformatics tools integrated into your web-platform. I will explain more detail: we have in our bioinformatics software UGENE a tool "Workflow designer". It has different elements for simple sequences operations as well as MSA algorithms, NGS analysis and so on. You can create new scheme in the workflow designer, set parameters that will be shown at new Galaxy tool window and then just generate tool config file. In Galaxy you can run this tool and get results at history panel and use it futher (in other Galaxy tools). I attached simple scheme example and showed how to generate config for it. Also there is a picture of our scheme in Galaxy. Exact answer is very interesting for us and we will hope to hear good response.

I will be grateful to you if this letter will be sent to correct address if that is not so.

Kind Regards, Peter Leontev, UGENE team

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