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?