how to use Trimmomatic on docker

[deo9...@gmail.com]

how to use how to use Trimmomatic  on docker, means because it need java to run, so can you please tell that

[Brian Haas]

There are a couple of ways to do this.

For some things, it might be easier to just work with the docker image interactively, like so:

 docker run --rm -it  -v`pwd`:`pwd` trinityrnaseq/trinityrnaseq bash

which gives you a bash prompt inside the docker container. It's mounted your current working directory, and you have access to all the software installed in it.

To access trimmomatic from within the trinity installation there, you could run:

java -jar /usr/local/bin/trinityrnaseq/trinity-plugins/Trimmomatic/trimmomatic.jar

'exit' to get out of the docker container.

If you don't want to work with the docker container interactively and would rather just run the trimmomatic command directly, you could do this:

docker run  -v`pwd`:`pwd` trinityrnaseq/trinityrnaseq java -jar /usr/local/bin/trinityrnaseq/trinity-plugins/Trimmomatic/trimmomatic.jar 

This looks like a good reference for you if you're planning to do a lot of docker work:

https://github.com/eduleboss/the-best-docker-books/tree/master/books

On Fri, Jan 25, 2019 at 12:41 PM <deo9...@gmail.com> wrote:

how to use how to use Trimmomatic  on docker, means because it need java to run, so can you please tell that

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Brian J. Haas
The Broad Institute
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[deo deo]

Awesome, thanks!