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Trinity in Docker
Run Trinity Using Docker
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.
% docker run -v`pwd`:`pwd` trinityrnaseq/trinityrnaseq \ /usr/local/src/trinityrnaseq/util/align_and_estimate_abundance.pl