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Create working folder and copy data

Let’s create an interactive session on the HPC:

qsub -I -S /bin/bash -l walltime=10:00:00 -l select=1:ncpus=2:mem=4gb

Let’s create working folders for today. Copy and paste the following block of code into your terminal and hit enter for the last command:

mkdir -p $HOME/workshop/ONTvariants
mkdir -p $HOME/workshop/ONTvariants/data
mkdir -p $HOME/workshop/ONTvariants/scripts
mkdir -p $HOME/workshop/ONTvariants/runs/run1_QC
mkdir -p $HOME/workshop/ONTvariants/runs/run2_mapping
mkdir -p $HOME/workshop/ONTvariants/runs/run3_variant_calling

Install tools using conda

Create a conda environment

Create a conda environment called ONTvariants_QC

conda create -n ONTvariants_QC
Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.5.0

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /home/barrero/miniconda3/envs/ONTvariants_QC



Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate ONTvariants_QC
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Let’s activate the conda environment:

conda activate ONTvariant_QC

Next, we need to install few tools for today’s exercises. Now let’s go the https://anaconda.org and search for the following tools and instructions on how to install them:

nanoplot, porechop_abi, chopper

For example, search for nanoplot:

image-20240517-045848.png

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:

image-20240517-050025.png

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:

image-20240517-050058.png

Copy and paste the first command shown above in your terminal where you have activated the ‘ONTvariant’ conda environment (Approx. 5-10min):

conda install bioconda::nanoplot

Now repeat the process for porechop_abi (Approx. 1min)’, then install it (Approx. 1min):

conda install bioconda::porechop_abi

Next, let’s install chopper (Approx. 1min):

conda install bioconda::chopper

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