Finding a public galaxy instance with a specific tool

Question: Finding a public galaxy instance with a specific tool

2.6 years ago by

United States

tymiller • 60 wrote:

Hi,

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?

Thanks!! Ty

ngs.plot chip-seq • 889 views

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modified 2.6 years ago • written 2.6 years ago by tymiller • 60

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

ADD REPLY • link written 2.6 years ago by robert.slany • 20

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!

ADD REPLY • link written 2.6 years ago by tymiller • 60

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?

ADD REPLY • link written 2.6 years ago by tymiller • 60

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/2.2.1.0 and if you visit it you will get a response of ["0.0.6", "0.0.7", "2.2.1.0"] 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.

ADD REPLY • link written 2.6 years ago by Martin Čech ♦♦ 4.9k

2.6 years ago by

Mo Heydarian ♦ 830

United States

Mo Heydarian ♦ 830 wrote:

Hi Ty,

Have you considered launching a Cloudman instance and loading NGS.plot from the toolshed?

You can launch a Cloudman from the launch page ( launch.usegalaxy.org ) using an Amazon Web Services account. Tools in the toolshed can be loaded to Cloudman instances, as well as local instances of Galaxy. The instance can be shutdown when you're finished with your analysis.

ADD COMMENT • link modified 2.6 years ago • written 2.6 years ago by Mo Heydarian ♦ 830

That is so helpful!! I had no idea it would be that easy to create my own galaxy instance. Works great, thanks!

ADD REPLY • link written 2.6 years ago by tymiller • 60

2.6 years ago by

Martin Čech ♦♦ 4.9k

United States

Martin Čech ♦♦ 4.9k wrote:

Sadly, there is no easy way to get this information. I have implemented an API endpoint recently that allows you to detect whether given tool is installed and what versions are available ( see https://usegalaxy.org/api/tools?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.0 ) However we did not implement a unified UI for grabbing all these from the public server list yet.

As of the tool comparison, I cannot help. :/

ADD COMMENT • link modified 2.6 years ago • written 2.6 years ago by Martin Čech ♦♦ 4.9k

2.6 years ago by

tymiller • 60

United States

tymiller • 60 wrote:

Hi Mohammad,

Do you know if the CloudMan Galaxy instance comes installed with reference genomes (specifically hg19)? I keep getting an error with this tool that seems like it can't find a dataset it needs, but I've given it everything else. I can't find anywhere that galaxy lists the reference genomes installed. I used "Cluster with Galaxy" when I set it up and I have all the tools on the main usegalaxy instance.

Thanks! Ty

ADD COMMENT • link written 2.6 years ago by tymiller • 60

What tool are you seeing this issue with?

ADD REPLY • link written 2.6 years ago by Mo Heydarian ♦ 830

NGS.plot It's a tool I installed from the toolshed https://toolshed.g2.bx.psu.edu/repository?repository_id=1838f2840adb4f23&changeset_revision=f7debdafc7cb

ADD REPLY • link written 2.6 years ago by tymiller • 60

So here is the issue. I'm pretty sure the most common reference genomes were installed when the cloudman galaxy instance was created - including hg19. However the tool doesn't recognize them as being available (the place to select the reference genome doesn't give a dropdown menu, you can just type into it. Even when typing no options come up.).

For newly installed tools, is there a way to direct them to the previously installed reference genomes?

ADD REPLY • link written 2.6 years ago by tymiller • 60

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