Trinity in Docker

Brian Haas edited this page Apr 25, 2017 · 7 revisions

Run Trinity Using Docker

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 Trinity like so:

% docker pull trinityrnaseq/trinityrnaseq

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

% docker run --rm -v`pwd`:`pwd` trinityrnaseq/trinityrnaseq Trinity \
      --seqType fq --single `pwd`/reads.fq.gz \
      --max_memory 1G --CPU 4 --output `pwd`/trinity_out_dir

Downstream analyses using Dockerized Trinity:

Trinity is installed in the Docker container at '/usr/local/src/trinityrnaseq'.

Just use that path to access all tools installed within Trinity.

eg.

 %  docker run -v`pwd`:`pwd` trinityrnaseq/trinityrnaseq \
      /usr/local/src/trinityrnaseq/util/align_and_estimate_abundance.pl
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