TrinityFusion Docker or Singularity

Run TrinityFusion Using Docker or Singularity

If you have Docker installed, you can pull our image from DockerHub, which contains Trinity and all software used for downstream analyses supported within the larger Trinity framework.

Pull the latest Docker image for TrinityFusion like so:

% docker pull trinityctat/trinityfusion

Run TrinityFusion like so (eg. as shown where with a very small test data set):

    % docker run --rm \
      -v `pwd`:/data \
      -v /path/to/ctat_genome_lib_build_dir:/ctat_genome_lib:ro \
      trinityctat/trinityfusion \
      /usr/local/src/TrinityFusion/TrinityFusion \
      --left_fq /data/reads_1.fq.gz \
      --right_fq /data/reads_2.fq.gz  \
      --output_dir /data/TrinityFusion-UC_outdir-Docker \
      --chimeric_junctions /data/Chimeric.out.junction \
      --aligned_bam /data/Aligned.out.bam \
      --genome_lib_dir /ctat_genome_lib

Running TrinityFusion Using Singularity

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

    %  singularity exec -e \
          -B /path/to/ctat_genome_lib_build_dir:/ctat_genome_lib:ro \
          TrinityFusion.simg \
          /usr/local/src/TrinityFusion/TrinityFusion \
          --left_fq reads_1.fq.gz \
          --right_fq reads_2.fq.gz \
          --output_dir TrinityFusion-UC_outdir-Singularity \
          --chimeric_junctions Chimeric.out.junction \
          --aligned_bam Aligned.out.bam \
          --genome_lib_dir /ctat_genome_lib