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Question: Custom tool error, results have been output, but galaxy error.
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gravatar for chenzhuod
6 months ago by
chenzhuod • 30
chenzhuod • 30 wrote:

Hi,

I have a custom tool, WGCNA, an R package to construct co-expression network.

and in galaxy output file, it has output results. But galaxy shows an error (But it doesn't show what error) :

Loading required package: dynamicTreeCut
Loading required package: fastcluster

Attaching package: 'fastcluster'

The following object is masked from 'package:stats':

    hclust

Attaching package: 'WGCNA'

The following object is masked from 'package:stats':

    cor

Loading required package: methods
Loading required package: sp

Attaching package: 'raster'

The following object is masked from 'package:WGCNA':

    blockSize
rna-seq tool development planeno custom • 212 views
ADD COMMENT • link •
modified 6 months ago by Jennifer Hillman Jackson ♦ 25k • written 6 months ago by chenzhuod • 30
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gravatar for Jennifer Hillman Jackson
6 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Use Planemo for Galaxy tool development and publishing. It includes many debugging functions.

Also, you might need better/more error trapping in your new tool. Success/fails tests at each step is the extreme while defaulting to system errors is the opposite. Somewhere in the middle is what most developers to decide on as a strategy. Not only do you want the tool to work under the best of circumstances, but you'll want it to capture critical failure points and report that back both to scientific users (ideally, actionable information that is available the GUI) and to developers/admins in the logs or stdout/stderr, to aid with troubleshoot configuration and related issues.

The above makes tools more robust. Smart tool tests that address not only configuration but also usage/content are a bonus and can impact how popular/robust a tool is perceived. Planemo can help construct tests.

Thanks! Jen, Galaxy team
ADD COMMENT • link modified 6 months ago • written 6 months ago by Jennifer Hillman Jackson ♦ 25k
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