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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 install bioconda::sniffles

FinallyNext, let’s install minimap2 and seqkit:

conda install bioconda::minimap2

conda install bioconda::seqkit

Now we are done installing all the tools that we need for today.

Approach #2 (we are not doing this - this just for your information) - installing all tools at once (slower option!)

Prepare the following environment.yml file:

name: ONTvariants
channels:
  - conda-forge
  - defaults
  - bioconda
dependencies:
  - samtools=1.20
  - sniffles=1.0.12
  - minimap=2-2.28
  - tabixseqkit=02.28.61

Create a new environment:

conda env create -f environment.yml

Installing more tools or dealing with compatibility issues between tools

As you have seen, we can search at anaconda.org for other tools that we might be interested to use.

Remember, if you run into compatibility issues or errors, you can always create a new conda environment for the tool of interest. NOTE: you can switch between conda environements as follows:

conda activate myenvironment1
#... do so work with it
conda deactivate
#now we can activate another environment
conda activate myenvironment2
#... do some other tasks
conda deactivate #optional to deactivate last environment to use given that when we submit a job to the HPC cluster it will be closed automatically at the completion of the last task.

Hands-on exercises

Exercise #1: running a test using a sample dataset

Convert the sam file to bam (a binary sam format) using samtools’ view command
Sort the bam file (needed for fast access) using samtools sort command
Create an index of the bam file (needed by IGV) using samtools index command

...