Problems Installing Mothur Suite on MAC OSX: Result > dependencies are not available through Bioconda

lupetti · March 14, 2019, 8:21am

Hi,

I’m trying to install the mothur suite on my local Galaxy (newest version), but I’m running into troubles. When I attempt to install it, my Galaxy stops working. Then I tried to install a single components through the repository, but it has troubles to install the mothur (1.39) dependency. In the terminal I’m getting this message:

PackageNotFoundError: Packages missing in current channels:

mothur

We have searched for the packages in the following channels:

Please help me, I do not want to be mothurless any longer.

jennaj · March 14, 2019, 4:48pm

Hi, I asked for some feedback/help from the tool authors at the IUC Gitter chat, feel free to join the chat there, or they might get back here: https://gitter.im/galaxy-iuc/iuc?at=5c8a830fd3b35423cbbaa805

Just to clarify a few items that will help with troubleshooting:

Are you running the stable branch of the 19.01 Galaxy release?
Was this a new install or an upgrade from a prior release? Which version?
Have other tools installed correctly since the install/upgrade?
Are you running Galaxy inside a virtualenv?
Are you using the default dependency resolvers or have you made changes? A new 19.01 install has some improvements for dependency resolving with conda.
More about Dependency Resolvers in Galaxy.

lupetti · March 15, 2019, 11:02am

I was running Galaxy 19.04, but I tried it now with the stable branch of the 19.01 Galaxy release with the same result. Both of them were a new install. I’ve tried to install other tools (with dependencies) and for them it worked.
I’m running Galaxy inside a virtualenv. I guess I use the default dependency resolvers, because I haven’t changed the settings.
I will check out gitter. Thank you very much for your help.

lupetti · March 28, 2019, 7:54am

If someone has the same issue: I was trying to install it on my mac, while mothur is not available for macOS in Bioconda

jennaj · March 28, 2019, 5:00pm

Thanks for posting that information back to the thread!

I saw your chat about this at Gitter, and the end result was certainly unexpected! I’m going to mark your reply as the solution so others that run into the same problem can find the remarks.