Question: Error when trying to create heatmap
gravatar for psu19
2.5 years ago by
psu190 wrote:

Hello. I am new to galaxy and trying to learn. I am trying to recreate the heatmap here:

by uploading a compressed tabular formatted text file to galaxy. When attempting to create a clustered heatmap under the "charts" option, I run into an error reading "This job was terminated because it used more memory than it was allocated."

When I try to use the heatmap tool under the regional variation set of tools I get an error reading:

"bash: /galaxy/main/shed_tools/ No such file or directory"

Any suggestions for how I can get around these two errors so that I can re create the heatmap would be greatly appriciated. Thanks.

ncbi geo heatmap geo • 796 views
ADD COMMENTlink modified 22 months ago by Jennifer Hillman Jackson25k • written 2.5 years ago by psu190

Hello, I see what I believe is your bug report or at least one that is related. Investigating the second error. Feedback soon.

The first error has to do with the size of the data and available resource for such jobs at Section 2.8 of the Galaxy support wiki explains alternatives for working with data/jobs that exceed the compute resources at

Jen, Galaxy team

ADD REPLYlink written 2.5 years ago by Jennifer Hillman Jackson25k
gravatar for Jennifer Hillman Jackson
22 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Sorry, forgot to post back. This tool has known dependencies issues that are now tracked. Please see this other recent post about this tool's status and alternatives:

I know that you tried the Charts heatmap option already and ran into memory problems. But perhaps the local/cloud Galaxy option worked out for you.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 22 months ago by Jennifer Hillman Jackson25k
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