Heatmap of numeric data tool produced error (usegalaxy and local)

Question: Heatmap of numeric data tool produced error (usegalaxy and local)

22 months ago by

vebaev • 130

vebaev • 130 wrote:

Hi, I got the following error on usegalaxy and also on my local galaxy:

bash: /galaxy/main/shed_tools/toolshed.g2.bx.psu.edu/repos/guru-ananda/heatmap/89902ebc58b9/heatmap/heatmap//galaxy/main/shed_tools/toolshed.g2.bx.psu.edu/repos/guru-ananda/heatmap/89902ebc58b9/heatmap/r_wrapper.sh: No such file or directory

My input file is tabular looking like this (coming from Deseq2 normalization table):

ath-miR168b-5p  1023.00925520949    1452.49907802224
ath-miR167d 168.658282615618    86.0793776317961
ath-miR165b 96.7711457630597    7.23356114552909
ath-miR8175 5.52977975788912    13.0204100619524

heatmap • 702 views

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modified 22 months ago by Jennifer Hillman Jackson ♦ 25k • written 22 months ago by vebaev • 130

Hello, The problem is likely due to the float values. I am running a few tests with your sample data. More feedback soon with how to use properly. Making sure that the tool is not problematic is part of this testing. Thanks for reporting the issue, Jen, Galaxy team

ps: If you would like to send in a bug report for the failed run at http://usegalaxy.org, now before I finish testing, that can speed up the troubleshooting and back-n-forth if I cannot reproduce the problem with the given data. Please include a link to this post thread in the comments of the bug submission so that the two can be linked. https://wiki.galaxyproject.org/Support#Reporting_tool_errors

ADD REPLY • link written 22 months ago by Jennifer Hillman Jackson ♦ 25k

Thanks for sending in the bug report so quickly - I'll use it for testing. Jen

ADD REPLY • link written 22 months ago by Jennifer Hillman Jackson ♦ 25k

22 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

I was able to confirm that your error is related to a known tool issue that is undergoing review/correction. Follow progress here: https://github.com/galaxyproject/galaxy/issues/3030

Thanks for reporting the problem! Jen, Galaxy team

ADD COMMENT • link written 22 months ago by Jennifer Hillman Jackson ♦ 25k

Thanks, I subscribed to the thread at github.

ADD REPLY • link written 22 months ago by vebaev • 130

Any news on the fix?

ADD REPLY • link written 22 months ago by vebaev • 130

Updates will post to the shared Github ticket. I just checked it and so far there has been no action.

The original tool author can also be contacted about problems. Do this through the Tool Shed. Log in, navigate to the tool, and in the upper right corner menu named "Repository Actions" there is the option to contact the repository owner. The repository probably has outdated or potentially incompatible dependencies when used with the newer releases of Galaxy.

There are other ways to graph a heatmap from tabular data within Galaxy. Within the dataset box, click on the "Visualize" icon (small graph icon, near the download disc icon), and choose "Charts". There are two heatmap options.

The DeepTools suite also has heatmap graphing options. These have a more specialized usage, but perhaps worth a look.

ADD REPLY • link modified 22 months ago • written 22 months ago by Jennifer Hillman Jackson ♦ 25k

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