ONTvariants - QC

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

Install tools using conda

Approach #1 - installing tools one at a time (faster option)

Create a conda environment called sniffles

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:

conda install bioconda::nanoplot