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Environmental Viral Detection pipeline. Contains VirSieveAlign, VirSieveGATK, VirSieveIVar, and VirSieveVEP applications

Environment Modules

Run module spider VirSieve to find out what environment modules are available for this application.

System Variables

  • HPC_VIRSIEVE_DIR - installation directory
  • HPC_VIRSIEVE_BIN - installation directory

Additional Information

Each tool expects to be given a path to a working folder where your configurations, FASTA files, custom references, etc. are located. To aid with this, UFRC provides a "wrapper script" for each application in the pipeline that can be called with a path pointing to your working directory. For example, to call VirSieveIVar to process the working directory /blue/groupname/username/virsieve_test/:

$ module load virseive/20210406
$ VirSieveIVar /blue/groupname/username/virsieve_test/

Each tool also has the ability to set non-default options via environment variables. Since we are running these tools within Singularity containers, you will need to prefix those environment variables with "SINGULARITYENV_" if you want to use them as overrides. For example, VirSieveIVar allows for a custom reference BED file by setting the PRIMERBED environment variable. To use "mycustom.bed" as a custom BED file in HPG, you would:

$ module load virsieve/20210406
$ export SINGULARITYENV_PRIMERBED=/path/to/mycustom.bed
$ VirSieveIVar /blue/groupname/username/virsieve_test/

The expected working directory structure and lists of the available environment variables for each tool can be found on that tool's page:

Job Script Examples

Expand this section to view script example.

#SBATCH --job-name=virsieve_test
#SBATCH --mail-type=NONE
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --mem-per-cpu=4gb
#SBATCH --time=24:00:00
#SBATCH --output=virsieve_test.log


cd ${TEST_PWD}
module load virsieve

# Remove any previous test results, create a working directory, and copy
# initial test reads into the expected position in working directory
if [ -d ${TEST_WORKDIR} ]; then rm -rf ${TEST_WORKDIR}/; fi
mkdir -p ${TEST_WORKDIR}/rawFASTQ

echo "Starting test run at $(date) on $(hostname)..."

# Run VirSieveAlign (rawFASTQ/ --> processedFASTQ/, mergedBAM/, rawBAM/)
VirSieveAlign ${TEST_WORKDIR}

# Run VirSieveIVar (mergedBAM/ --> primerTrimBAM/)
# export SINGULARITYENV_PRIMERBED=/path/to/mycustom.bed

# Run VirSieveGATK (primerTrimBAM/ --> filteredVCF/, alignmentArtifactFilteredVCF/, etc.)

# Run VirSieveVEP (filteredVCF/, alignmentArtifactFilteredVCF/ --> vepOutputs/, results/)

# There should be some files in the results/ directory
echo "There should be some results listed below:"
find ${TEST_WORKDIR}/results/ -type f ! -empty -ls

echo "Test complete at $(date)."