Revision as of 19:58, 27 May 2022 by Israel.herrera (talk | contribs) (Israel.herrera moved page VirSieve to VirSIeve)
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VirSieve website  

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

See the VirSieve_Job_Scripts page for VirSieve Job script examples.