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 ONTvariant
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/ONTvariant
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate ONTvariant
#
# To deactivate an active environment, use
#
# $ conda deactivate
Let’s activate the conda environment:
conda activate ONTvariant
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:
samtools, sniffles, minimap2
For example, search for samtools:
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:
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:
Copy and paste the first command shown above in your terminal where you have activated the ‘ONTvariant’ conda environment:
conda install bioconda::samtools
Now repeat the process for ‘sniffles’, then install it:
conda install bioconda::sniffles
Finally, let’s install minimap2:
conda install bioconda::minimap2
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 - tabix=0.2.6
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
Ecoli