Question: Running DESeq2 inside local Galaxy instance
0
gravatar for gkuffel22
13 months ago by
gkuffel22170
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 • 564 views
ADD COMMENTlink modified 5 weeks ago by jkoral100 • written 13 months ago by gkuffel22170
1

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 13 months ago by Devon Ryan1.9k

Devon's advice is good, please start here.

ADD REPLYlink written 13 months ago by Martin Čech ♦♦ 4.6k

Hi all, I have been working with Gina on this and we are using the latest version of Galaxy 18.01 and are strictly using Conda for dependency resolution. But when I go to install DeSeq2, I see all the dependencies are resolved through Conda except bioconductor-deseq2. The version shows None and under Installation Status, there is a red ! with the message "Dependency resolved, but version None not found"

Ideas?

ADD REPLYlink written 5 weeks ago by jkoral100

Odd, I suspect that there was an error when creating the conda environment. You can try removing it (as the galaxy user on the command line) and reinstalling it (preferably via Galaxy). Worst case scenario, one of us can give you our environment.yaml.

ADD REPLYlink written 4 weeks ago by Devon Ryan1.9k
0
gravatar for jkoral
5 weeks ago by
jkoral100
United States
jkoral100 wrote:

Hi all, I have been working with Gina on this and we are using the latest version of Galaxy 18.01 and are strictly using Conda for dependency resolution. But when I go to install DeSeq2, I see all the dependencies are resolved through Conda except bioconductor-deseq2. The version shows None and under Installation Status, there is a red ! with the message "Dependency resolved, but version None not found"

Ideas?

ADD COMMENTlink written 5 weeks ago by jkoral100
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