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Question: gplots R getting run error
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gravatar for mateusbellomo
3.0 years ago by
mateusbellomo • 10
mateusbellomo • 10 wrote:

Hello,

 

I'm developed a tool to generate a heatmap using heatmap.2() function from gplots of R. Unfortunately I'm getting an error when I try to execute it in Galaxy. When I run the tool from terminal it works perfectly though. I think it's because the gplots package of R because when I comment it's declaration the error stops.

 

I cant post the Galaxy error here because somehow Galaxy is showing me an old error when I get this one (it happened before and I think it's a bug but I'm not sure if occurs just in my installation).

 

Thanks in advance
gplots R • 886 views
ADD COMMENT • link •
written 3.0 years ago by mateusbellomo • 10
0
gravatar for Jennifer Hillman Jackson
3.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Is the job failing or is something odd occuring in the user interface? 

Many factors can be involved to get newly wrapped tools to functions correctly. Are you following a specific tutorial (from the Wiki) or other existing wrapper as a guide (ideally one from the Tool Shed)?

As a guess, double check that the galaxy user has the version of R you are targeting in its PATH.

We can start there, but also know that the developers mailing list can be a good resource: galaxy-dev@lists.galaxyproject.org https://wiki.galaxyproject.org/MailingLists

Jen, Galaxy team
ADD COMMENT • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k

Actually the job is failing. I'm not using any specific tutorial (I didn't find a specific tutorial in R tools) and any wrapper as a guide (could you please indicate me some?). I think it's something to do to 'gplots' package because I already tested other R functions and it worked.

I'm trying to execute the tool in my local copy of Galaxy so I think the R path is correct.

ADD REPLY • link written 3.0 years ago by mateusbellomo • 10

There are tool development tutorials in the first wiki link I shared plus this is a tool that calls R created by the devteam (as an example)  https://toolshed.g2.bx.psu.edu/view/devteam/xy_plot/23657fcaaa5c

I personally do not know why gplots would be different than the other functions for use in Galaxy, but someone else may know/reply.

Hopefully this helps, Jen

ADD REPLY • link modified 3.0 years ago • written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k
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