If you have Docker installed, you can pull our image from DockerHub, which contains TransDecoder and all software used for execution.

Pull the latest Docker image for TransDecoder like so:

% docker pull trinityrnaseq/transdecoder

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

% docker run --rm -v`pwd`:`pwd` trinityrnaseq/transdecoder TransDecoder.LongOrfs ...parameters...

and

% docker run --rm -vpwd:pwd trinityrnaseq/transdecoder TransDecoder.Predict ...parameters...

Important: specify the complete path to the output directory when using Docker (--output_dir | -O )

see main documentation for TransDecoder usage

Both BLAST+ and HMMER are installed in the Docker container at '/usr/local/bin', which is included in the PATH setting.

example execution:

 %  docker run -v`pwd`:`pwd` trinityrnaseq/transdecoder blastp ...parameters...

see main documentation for TransDecoder usage

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

    %  singularity exec -e TransDecoder.simg  TransDecoder.LongOrfs ...parameters... 

see main documentation for TransDecoder usage

accessing other tools used by TransDecoder is simply like above using that program name