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Question: New tool error - could not find function from (R) bioconda package
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gravatar for testtoolshed
15 months ago by
testtoolshed • 30
testtoolshed • 30 wrote:

Hi, I've tried to develop new tool based on getGenomicRatioSetFromGEO function from bioconductor-minfi package. It works for me on my computer but didn't work on galaxy and return Fatal error: Exit code 1 () Error: could not find function "getGenomicRatioSetFromGEO" Execution halted Is it R version issue or maybe you have some different ideas why my tool doesn't work?
error bioconda new tool R • 562 views
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modified 15 months ago by Jennifer Hillman Jackson ♦ 25k • written 15 months ago by testtoolshed • 30
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gravatar for Jennifer Hillman Jackson
15 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

You might need to add the correct R function/dependency to your tool wrapper, so that it is installed along with the tool (using conda). This will make it a more robust tool especially if you plan to contribute it to the tool shed. It is possible to just install the R dependency, makes sure the tool and Galaxy have access to it in the ENV/PATH settings, but that is a custom method.

Also see how to use Bioblend for tool development here: https://galaxyproject.org/tools/

Thanks, Jen, Galaxy team
ADD COMMENT • link written 15 months ago by Jennifer Hillman Jackson ♦ 25k
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