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ctat_mutations_docker_singularity
You can import a preconfigured CTAT-Mutations for GRCh38 from Dockstore
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
![](https://raw.githubusercontent.com/wiki/trinityrnaseq/trinityrnaseq/images/singularity_logo.png)
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'