Let’s create an interactive session on the HPC:
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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
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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:
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name: ONTvariants channels: - conda-forge - defaults - bioconda dependencies: - samtools=1.20 - sniffles=1.0.12 - minimap=2-2.28 - tabix=0.2.6 |
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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:
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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
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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 |
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