Question: Heatmap of numeric data tool produced error (usegalaxy and local)
0
gravatar for vebaev
22 months ago by
vebaev130
vebaev130 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
ADD COMMENTlink modified 22 months ago by Jennifer Hillman Jackson25k • written 22 months ago by vebaev130

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 REPLYlink written 22 months ago by Jennifer Hillman Jackson25k
1

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

ADD REPLYlink written 22 months ago by Jennifer Hillman Jackson25k
0
gravatar for Jennifer Hillman Jackson
22 months ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 22 months ago by Jennifer Hillman Jackson25k

Thanks, I subscribed to the thread at github.

ADD REPLYlink written 22 months ago by vebaev130

Any news on the fix?

ADD REPLYlink written 22 months ago by vebaev130

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 REPLYlink modified 22 months ago • written 22 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 175 users visited in the last hour