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nickjcroucher / gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
http://nickjcroucher.github.io/gubbins/
GNU General Public License v2.0
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Unable to install gubbin #399

Closed dzc0104 closed 2 months ago

dzc0104 commented 3 months ago

Hi,

I was trying to install Gubbins through the Recommended installation method - conda and OSX/Linux - installing from the repository in my local terminal. I had downloaded and installed anaconda3.

The error that I am getting is the package for gubbin is not found.

I have attached hereby the word file which contains what I did. Please find the attachment. Gubbin install troubleshoot.docx

nickjcroucher commented 3 months ago

I would try replacing conda with mamba - that should solve the environment, although there do appear to be problems installing the latest version, as identified by other issues.

dzc0104 commented 3 months ago

Thanks for the response @nickjcroucher, I tried with mamba using the command line

1)conda install -n base -c conda-forge mamba 2)mamba create -n myenv python=3.8 3) mamba activate myenv 4)mamba init : (error: package not found and permission denied) 5)mamba install gubbin (following package could not be installed)

6)sudo mamba init 7)mamba install -c conda-forge -c bioconda gubbin (package could not be installed)

8)mamba activate base. Run 'mamba init' to be able to run mamba activate/deactivate and start a new shell session. Or use conda to activate/deactivate (error: package not found)

I'm still facing problems. Am I missing something here to troubleshoot it?

nickjcroucher commented 3 months ago

Does mamba install gubbins work?

dzc0104 commented 3 months ago

It said the following package could not be installed. @nickjcroucher

nickjcroucher commented 3 months ago

Please try to install v3.3.5, released on conda today.

nickjcroucher commented 2 months ago

Please reopen if there is still a problem.