Question

Running DESeq2 inside local Galaxy instance

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gkuffel ▴ 10

@gkuffel-12871

Last seen 6.0 years ago

Loyola University

Hi everyone,

We have tried many times to install DESeq2 to our local instance of Galaxy. The install is successful but when we run the tool we get the following error:

Fatal error: An undefined error occurred, please check your input carefully and contact your administrator.
Error in library("getopt") : there is no package called ‘getopt’

Now, upon closer inspection I do see that bioconductor-deseq2 is listed as a dependency and that dependency was not resolved in the installation. I don't know where to get this dependency in Galaxy as when I search for it in the tool shed there are many bioconductor packages available (edgeR, limma..) but nothing for DESeq2. Has anyone ran into this issue or have any ideas?

deseq2 galaxy • 1.5k views

ADD COMMENT • link 7.7 years ago gkuffel ▴ 10

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Thanks, I was trying to get some input from the author of the tool, Michael Love and thought this forum would be the best place to reach him.

ADD REPLY • link 7.7 years ago gkuffel ▴ 10

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I don't have any additional ideas beyond what Jim pointed out. If you get stuck contact Galaxy for help.

ADD REPLY • link 7.7 years ago Michael Love 43k

score 1 · Answer 1 · 2017-04-20

This doesn't really seem like a Bioconductor question. You are trying to do stuff with a local Galaxy installation, and that installation is failing because you don't have the CRAN getopt package installed. I would imagine installing the missing package would be the first step, and if you have further questions, probably you should be asking on whatever help forum exists for Galaxy.