Developing tool from web app

Question: Developing tool from web app

4.1 years ago by

Spain

Hello everyone. I'm new to Galaxy. We intend to install a local Galaxy Server to process data. But as the first step of the pipeline, we need to use a web App we have already developed. We thought that having the servlet already ready, the Galaxy tool would just need to call the url.

I have been reading a lot from the wiki, like https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial and https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Coutputs.3E_tag_set , but I haven't been able to find answers to my particular problem.

So if anyone know how to create a tool from an existing web App, I would be really thankful.

Thanks a lot in advance,

Nicolas.

tool development • 971 views

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modified 4.1 years ago • written 4.1 years ago by nicolas.lucero145 • 40

4.1 years ago by

jmchilton ♦ 1.1k

United States

jmchilton ♦ 1.1k wrote:

Your best best is probably to develop a data source tool - this is outlined on the wiki and there are a bunch of examples in the code base itself - including the GenomeSpace tools, the UCSC Table Browser, and the Intermine tools.

Other approaches I have used before is to use the web app itself to push data into Galaxy - you said servlet so I assume this is something on the JVM - pushing data from an external application into Galaxy is exactly the use case that drove me to initially write blend4j.

Finally, if you have identifiers and a consistent API to your webapp sometimes it is easiest to just write a simple tool to fetch data. Here is an example of such a tool I wrote for the Galaxy-P project awhile ago.

ADD COMMENT • link written 4.1 years ago by jmchilton ♦ 1.1k

4.1 years ago by

nicolas.lucero145 • 40

Spain

nicolas.lucero145 • 40 wrote:

Thanks a lot. I will check the source right away. I'll post later what I ended up doing.

ADD COMMENT • link written 4.1 years ago by nicolas.lucero145 • 40

4.1 years ago by

nicolas.lucero145 • 40

Spain

nicolas.lucero145 • 40 wrote:

I using blend4j, trying to push data from my app into Galaxy. But I couldn't find any method that allows me to use an URI instead of a File source. Is there something I'm missing?

ADD COMMENT • link written 4.1 years ago by nicolas.lucero145 • 40

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