VirSorter2/en

VirSorter2 is a tool to identify new viral sequences.

This page discusses how to install and use VirSorter2 v2.2.4.

Source code and documentation for VirSorter2 can be found on their GitHub page.

Remember to cite VirSorter2 if you use it for your analyses.

Installing VirSorter2 in a Python virtual environment

These instructions install VirSorter2 in your $HOME directory using Alliance's prebuilt Python wheels. Custom Python wheels are stored in /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/. To install a VirSorter2 wheel, we will use the pip command and install it into a Python virtual environment.

1. Load the necessary modules.

   module load StdEnv/2020 python/3.8 hmmer/3.3.2 prodigal/2.6.3
   

2. Create and activate a Python virtual environment.

   virtualenv --no-download ~/ENV_virsorter
   source ~/ENV_virsorter/bin/activate
   

3. Install VirSorter2 v2.2.4 in the virtual environment.

   pip install --no-index --upgrade pip
   pip install --no-index virsorter==2.2.4
   

4. Validate the installation.

   virsorter -h
   

5. Freeze the environment and requirements set.

   pip freeze > ~/virsorter-2.2.4-requirements.txt
   

6. Download the database in $SCRATCH with the --skip-deps-install option to bypass conda installation and also because dependencies are already installed.

   virsorter setup --db-dir $SCRATCH/db -j 4 --skip-deps-install
   

Testing VirSorter2

1. Deactivate your virtual environment

   deactivate
   

2. Download the test dataset in $SCRATCH.

   wget -O $SCRATCH/test.fa https://raw.githubusercontent.com/jiarong/VirSorter2/master/test/8seq.fa
   

3. Create a submission script
   test-virsorter.sh

   #!/bin/bash
   
   #SBATCH --time=00:30:00
   #SBATCH --mem-per-cpu=2G
   #SBATCH --cpus-per-task=2
   
   # Load modules dependencies
   module load StdEnv/2020 python/3.8 hmmer/3.3.2 prodigal/2.6.3
   
   # Generate your virtual environment in $SLURM_TMPDIR
   virtualenv --no-download $SLURM_TMPDIR/ENV
   source $SLURM_TMPDIR/ENV/bin/activate
   pip install --no-index --upgrade pip
   
   # Install VirSorter2 and its dependencies
   pip install --no-index -r ~/virsorter-2.2.4-requirements.txt
   
   # Run VirSorter2 with the test dataset, using at most $SLURM_CPUS_PER_TASK and ignore conda.
   # The database must already exist and you must specify its location.
   virsorter run -w $SCRATCH/test.out -i $SCRATCH/test.fa --min-length 1500 -j $SLURM_CPUS_PER_TASK --verbose --use-conda-off --db-dir $SCRATCH/db all
   

4. Start an interactive job.

   salloc --mem-per-cpu=2G --cpus-per-task=2 --account=<your-account>
   # salloc: Granted job allocation 1234567
   bash test-virsorter.sh             # Run the submission script
   exit                               # Terminate the allocation
   # salloc: Relinquishing job allocation 1234567
   

Upon a successful test run, you can submit a non-interactive job with your own dataset using sbatch.