ctat_mutations_docker_singularity

CTAT-Mutations Docker and Singularity Images

CTAT-Mutations is available on Dockstore for plug/play with Cloud environments

You can import a preconfigured CTAT-Mutations for GRCh38 from Dockstore

Run Trinity Using Docker

If you have Docker installed, you can pull our image from DockerHub, which contains all software used for RNA-seq based variant calling in the Trinity CTAT Mutations Pipeline.

Pull the latest Docker image for CTAT Mutations Pipeline like so:

% docker pull trinityctat/ctat_mutations

Run the CTAT Mutations Pipeline like so (eg. as shown where with a very small test data set):

    % DATA_FOLDER=`pwd`
    % docker run --rm -v ${DATA_FOLDER}:${DATA_FOLDER} -v /tmp:/tmp \
         -v ${CTAT_GENOME_LIB}:/ctat_genome_lib_dir:ro \
         trinityctat/ctat_mutations \
        /usr/local/src/ctat-mutations/ctat_mutations \
        --left ${DATA_FOLDER}/reads_1.fastq.gz \
        --right ${DATA_FOLDER}/reads_2.fastq.gz \
        --sample_id test \
        --output ${DATA_FOLDER}/ctat_mutations_outdir \
        --cpu 10 \
        --genome_lib_dir /ctat_genome_lib_dir

Running Trinity Using Singularity

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

    %  DATA_FOLDER=`pwd`
    %  singularity exec -e -B ${DATA_FOLDER}:${DATA_FOLDER} -B /tmp:/tmp \
          -B ${CTAT_GENOME_LIB}:/ctat_genome_lib_dir:ro  \
            ctat_mutations.simg \
           /usr/local/src/ctat-mutations/ctat_mutations \
           --left ${DATA_FOLDER}/reads_1.fastq.gz \
           --right ${DATA_FOLDER}/reads_2.fastq.gz \
           --sample_id test \
           --output ${DATA_FOLDER}/example.HC.singularity \
           --cpu 10 \
           --genome_lib_dir /ctat_genome_lib_dir

If you have difficulty using the Singularity image that we provide, you can build one directly like so: 'singularity pull docker://trinityctat/ctat_mutations'