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Let’s create an interactive session on the HPC:
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Install tools using conda
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Create a conda environment
Create a conda environment called snifflesONTvariants_QC
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conda create -n ONTvariants_QC |
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nanoplot, porechop_abi, chopper |
For example, search for nanoplot:
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If the tool you are looking is available in conda, a list of options will be presented. Typically choose the option at the top with most downloads and compatible for your system:
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Click on the link to the tool of interest and you will be presented with the conda command line to run in your system to install the tool:
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Copy and paste the first command shown above in your terminal where you have activated the ‘ONTvariant’ conda environment (Approx. 5-10min):
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conda install bioconda::nanoplot |
Now repeat the process for porechop_abi (Approx. 1min)’, then install it (Approx. 1min):
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conda install bioconda::porechop_abi |
Next, let’s install chopper (Approx. 1min):
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conda install bioconda::chopper |