Question: Running DESeq2 inside local Galaxy instance
gravatar for gkuffel22
11 months ago by
United States
gkuffel22170 wrote:

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?

bioconductor galaxy deseq2 • 419 views
ADD COMMENTlink written 11 months ago by gkuffel22170

What version of Galaxy are you using? If you're using anything recent, switch to conda for dependency resolution and call it done. For me that's saved a LOT of headaches.

ADD REPLYlink written 11 months ago by Devon Ryan1.9k

Devon's advice is good, please start here.

ADD REPLYlink written 10 months ago by Martin Čech ♦♦ 4.4k
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