Question: bioconductor-cummerbund dependency will not resolve
gravatar for jkoral
7 months ago by
United States
jkoral100 wrote:

I have installed CuffDiff, but there is a failed dependency called bioconductor-cummerbund that will not resolve. When running a job in CuffDiff, I get the following error message. Conda dependency seemingly installed but failed to build job environment.

This is on a local instance and is running version 18.01 on Ubuntu 17.10.

Any ideas?

Thanks, Joe

ADD COMMENTlink modified 7 months ago by Jennifer Hillman Jackson25k • written 7 months ago by jkoral100
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson25k wrote:


The server log will have more details about what exactly the problem is. You also might want to double check your dependency resolvers, and if you modify them, test uninstalling then reinstalling the tool from the ToolShed and rerun to see if that helped. You also might want to check the dependency installation status in your local under Admin >> Tool Management >> Manage dependencies.

Note: There are some known issues with the Cuffdiff tool wrapper and a new CummeRbund wrapper is being developed. It is not clear if the error you reported is related or not, but it does mean that when using the existing tool wrapper a tool error can result when certain options are used.

I started a conversation in Gitter with the development team internally about this type of conda error as it has come up a few times. Please feel free to ask the question directly to the developers at the public Gitter chat Often troubleshooting this issue involves some back and forth and a chat is quicker.

Please share the area of the log reporting the problem if you cannot solve it. Paste the text at a public location with a shareable link - this makes it easier to read/review. Redact any content that is sensitive as needed. Gist is one common option You can post that here, or in the Gitter Galaxy chat room.

So, if you do open a Gitter chat, include the log link plus optionally a link to your question here for context. Please paste a link to that chat post back here as a reply comment (or if I see it, will post it back). This helps to consolidate related Q&A at the different support channels.

Help links for the above:

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 7 months ago • written 7 months ago by Jennifer Hillman Jackson25k
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