Virus Integration Finder (VIF) Installation Instructions

ctat-VIF leverages genome resources packaged as the CTAT genome library and built according to specific versions of the STAR Aligner. See the CTAT genome lib software compatibility matrix for access to genome libs and matching versions of STAR.

See instructions on Human-Virus-Database-Prep for integrating the needed viral genome resources into the CTAT genome library.

After having the CTAT genome lib unpacked, the viral resource supplements integraged, and the matching version of STAR installed, there's little else needed beyond the ctat-VIF software itself, which can be run in one of three ways - but know that Docker or Singularity are preferred since they come with everything you might need:

• downloading the ctat-VIF software package from the ctat-VIF downloads page.
• via Docker (see below)
• via Singularity (see below)

Docker

We provide a Docker image that contains all software pre-installed for running ctat-VIF and it's available here: https://hub.docker.com/r/trinityctat/ctat_vif/tags?page=1&ordering=last_updated

If you have docker installed, you can pull the image like so:

docker pull trinityctat/ctat_vif

ctat-VIF could be run like so via Docker:

# below we assume you have your reads_1.fq.gz and reads_2.fq.gz in your current working directory
# and also have the ctat_genome_lib_build_dir in your current directory.
# and of course your viruses.fasta file that you provide

docker run -v `pwd`:/data --rm trinityctat/ctat_vif \
    /usr/local/bin/ctat-vif \
    --sample_id ${sample_id} \
    --left /data/reads_1.fastq.gz \
    --right /data/reads_2.fastq.gz \
    --genome_lib_dir /data/ctat_genome_lib_build_dir \
    --outputdir ${sample_id}.ctat_vif_outdir

Singularity

Singularity is easier and safer to use than Docker, and is our preferred method for running ctat-VIF. All releases of ctat-VIF have a Singularity image (.simg) offered for download from our CTAT Singularity site. If you have Singularity installed and the .simg file downloaded, you can run STAR-Fusion like so:

singularity exec -e -B `pwd` -B /path/to/ctat_genome_lib_build_dir \
        ctat_vif.v${version}.simg \
        /usr/local/bin/ctat-vif \
        --sample_id ${sample_id} \
        --left /data/reads_1.fastq.gz \
        --right /data/reads_2.fastq.gz \
        --genome_lib_dir /data/ctat_genome_lib_build_dir \
        --outputdir ${sample_id}.ctat_vif_outdir