Provide all tools used by the pipeline

wodanaz / Assembling_viruses

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Provide all tools used by the pipeline #36

Closed johnbradley closed 3 years ago

johnbradley commented 3 years ago

The pipeline requires manual installation of seqtk and pangolin since there are no environment modules for these tools. Seqtk installs as a binary and can be easily added to the PATH. Pangolin requires a conda environment which requires additional steps before running the workflow on HARDAC:

start interactive session
load Anaconda3 module
activate the pangolin environment We should provide all the tools needed for the pipeline and avoid these extra steps.

johnbradley commented 3 years ago

To fix this I suggest a single conda environment that contains all the pipeline requirements. All of the tools we currently use are available as conda packages. This is also my plan for creating a container for issue #23.