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phac-nml / snvphyl-galaxy

SNVPhyl whole genome phylogenomics pipeline.
Apache License 2.0
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Verify_map error #34

Open PHemarajata opened 3 years ago

PHemarajata commented 3 years ago

Hi, I installed SNVPhyl on a new Galaxy instance and ran into this error during Verify Mapping Quality:

Failed to activate conda environment! Error was: Not a conda environment: /home/sysadmin/galaxy/galaxy/database/dependencies/_conda/envs/__snvphyl-tools@1.8.2

Any suggestion will be appreciated. Thank you!

apetkau commented 3 years ago

Hello @PHemarajata. Could you verify (within Galaxy) if the conda environment properly installed when you installed the tool? It looks like it did not get created. You could try uninstalling one of the SNVPhyl tools (e.g., verify_map) and then re-installing it again.

You can also try to install it yourself with:

/home/sysadmin/galaxy/galaxy/database/dependencies/_conda/bin/conda create --name __snvphyl-tools@1.8.2 -c bioconda -c conda-forge -c defaults snvphyl-tools=1.8.2

However, this is a more advanced solution and is only recommended if you are familiar with managing conda environments.