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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/repeatmaskerlibraries-20140131.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.

Docker Pull Command
Owner
robsyme
Source Repository