I've had this question several times over the last couple of years - is there a way to find a public galaxy instance that contains a specific tool that I would like to use?
I would really like to use NGS.plot on galaxy. It has been place in the tool shed https://toolshed.g2.bx.psu.edu/repository?repository_id=1838f2840adb4f23&changeset_revision=f7debdafc7cb so it is available to be installed. I don't have access to a local galaxy instance, so I would like to be able to use it on a public instance. Is there some way to search which public instances contain NGS plot?
On a side note, is there a tool that has the same functionality as NGS plot in the usegalaxy instance? Maybe computeMatrix with plotProfile?
Dear Galaxy curators,
I couldn't agree more. Please, add NGS.plot to usegalaxy.org. All my data are there already and for some applications this tool seems to be easier to use than deeptools.
Thank you very much Best Robert
I completely agree! I've been trying to use computeMatrix with plotProfile in combination to do something similar, but I can't get the same outputs. The collaborator who told me to use this is at the Broad, and they and their colleagues use it all the time in command line. I'm trying to get Pol2 ChIP-seq profile to measure traveling ratio/pausing index, and ngs.plot would be perfect.
Thanks for the response Martin! Unfortunately, I was not able to see what that link allowed me to do, as it did not lead to a usable tool - it was only an output of three columns and one row. Is it something I can use to find if this tool is installed on a particular public instance, even if one at a time?
that link is asking the Galaxy instance at usegalaxy.org whether it has a tool with a tool id of
tool_id=toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/220.127.116.11and if you visit it you will get a response of
["0.0.6", "0.0.7", "18.104.22.168"]which means it has three versions of that tool installed.
Unless you are able to write a script that would make this request to all public Galaxies with that API it won't help you much. Sorry. :/
We have plans for making this exact interface for searching tools and are not too far from it.