# Run Trinity Using Docker
If you have [Docker](https://www.docker.com/) installed, you can pull [our image from DockerHub](https://hub.docker.com/r/trinityrnaseq/trinityrnaseq/), 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 \
--left `pwd`/reads_1.fq.gz \
--right `pwd`/reads_2.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/bin/trinityrnaseq'.
Just use that path to access all tools installed within Trinity.
eg.
% docker run -v`pwd`:`pwd` trinityrnaseq/trinityrnaseq \
/usr/local/bin/trinityrnaseq/util/align_and_estimate_abundance.pl
>With the above, just be sure to specify full paths to inputs and outputs.
# Running Trinity Using Singularity
Singularity is easier and safer to use than Docker, and is our preferred method for running Trinity. All modern releases of Trinity have a Singularity image (.simg) offered for download from our [Trinity Singularity Image Archive](https://data.broadinstitute.org/Trinity/TRINITY_SINGULARITY/). If you have [Singularity](https://sylabs.io/docs/) installed and the .simg file downloaded, you can run Trinity like so:
```
% singularity exec -e Trinity.simg Trinity \
--seqType fq \
--left `pwd`/reads_1.fq.gz \
--right `pwd`/reads_2.fq.gz \
--max_memory 1G --CPU 4 \
--output `pwd`/trinity_out_dir
```
All downstream analyses can be accessed similarly to the Docker instructions above, but using the Singularity execution syntax.