Problem installing tool dependencies using Conda: Ubuntu 16.04 and python 2.7


I installed a tool from tool shed, But it can’t run properly on my Galaxy instance. Tool execution generated the following messages:

Please help me.

Thank you

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Hello @Wilsoncyx

There might have been a problem with how you initially installed Galaxy.

Please review this prior Q&A for the instructions, along with some troubleshooting help: Error when trying to run Galaxy on MacOs

If that doesn’t help, please share more details:

  1. Is this a new Galaxy instance?
  2. Did you use the master release of 19.01 (not a development or other branch)
  3. What is your OS? Mac or other? Which?
  4. Is this the first tool you have attempted to install or have others failed/succeeded?


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Hi jennaj,

I try to rebuild my Galaxy instance by use the methods from Error when trying to run Galaxy on MacOs

But it doesn’t help.

This is a new Galaxy instance installed on my personal computer. I use the master release of 19.01. It’s a new computer running Ubuntu 16.04 and python 2.7. I tried several native tools and they have no problems. This is the first tool I have attempted to install.

Thanks for your help!

I can’t install dependencies in the Manage dependencies menu. When I pressed install checked dependencies using Conda, the command line output a lot of about Dependency package not found information. Just like DEBUG 2019-04-17 01:00:28,771 [p:3445,w:1,m:0] [uWSGIWorker1Core3] Dependency rpy2 not found.

This issue may be related to previous issue.


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Did you delete your old Galaxy install, get a fresh git checkout, create a python venv (using python version 2.7), and then run sh for the first time?

If not, try deleting any existing Python/Conda venv, recreate the python version, and start up with sh It might work. If not, you’ll probably need to start over (more is misconfigured).

Make sure that you are using python version 2.7 – version 3 will not work yet. The error for rpy2 means that it cannot be found/used for some reason (not in your PATH? Or pointing to the wrong python version?).

Dependency resolves are described here:

When you check the Manage Dependencies page, what is the status of the dependencies of the Join tool? Can you provide more of the log output when you attempt to install the dependencies from that page? The log messages you’ve referred to happen when Galaxy tries to resolve dependencies, but there should be other messages when Galaxy tries to install them.