robsyme/repeatmasker-onbuild repository overview

⁠RepeatMasker-onbuild Container

This simple container is designed to make it easier to run RepeatMasker on new machines. If you have your own permanent big-ass-server⁠, you might want to simply install the software as usual and that's very sensible.

There are also plenty of situations were you might want to use a container:

• You are using compute resources on EC2 or GCE and you don't want to make a new disk image for each step of the annotation pipeline (and you don't want the hastle of cloud orchestration tools and scripts.
• A container described by a Dockerfile also provides complete documentation of how the results were generated, which makes replication a little easier.
• You are using a docker-aware pipeline⁠.

⁠What Does the Image Contain?

This images contains the RepeatMasker binary and its prerequisites hmmer, rmblast, blast+ and trf. It does not contain the RepBase database. You will need to register and downlod this yourself and then build a new image based on this one. It also does not contain the search engines Cross_Match and ABBlast/WUBlast because of licencing restrictions.

⁠Running RepeatMasker from inside a container

You'll need a copy of the latest Repbase-derived RepeatMasker libraries⁠ (requires free registration⁠), renamed as repeatmaskerlibraries.tar.gz. We then create a new Dockerfile and generate our new image

wget --user your_username \
    --password 12345 \
    -O repeatmaskerlibraries.tar.gz \
    http://www.girinst.org/server/RepBase/protected/repeatmaskerlibraries/RepBaseRepeatMaskerEdition-20170127.tar.gz
echo "FROM robsyme/repeatmasker-onbuild" > Dockerfile
docker build -t myrepeatmasker .

We can then run RepeatMasker:

docker run -v $PWD:/in -w /in myrepeatmasker RepeatMasker scaffolds.fasta

This runs the container, mounting the host's current directory (and all subdirectories) inside the container at /in (-v $PWD/in). The w /in arguments ensure that the command is run from this new directory. We then specify that we want to use the myrepeatmasker image we just created. Inside the container, the command RepeatMasker scaffolds.fasta is run.

⁠Modifying the container

You are free to modify the container (perhaps you really want to use Cross_Match, for example. Simply clone this repository (git clone https://github.com/robsyme/nextflow-annotate.git) and modify the Dockerfile before building.