TransDecoder_Docker_or_Singularity

Run TransDecoder Using Docker

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

Optional analyses available via Dockerized TransDecoder:

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

Running TransDecoder Using Singularity

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