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README.md

Dfam TE Tools Container

Dfam TE Tools includes RepeatMasker, RepeatModeler, and coseg. This container is an easy way to get a minimal yet fully functional installation of RepeatMasker and RepeatModeler and is additionally useful for testing or reproducibility purposes.

You should consider using the Dfam TE Tools container if:

  • You or your computing environment already use docker or singularity
  • You are uncomfortable compiling dependencies by hand or have had problems doing so
  • You do not need to use any of the other tools (e.g. RMBlast, HMMER) for anything besides RepeatMasker and RepeatModeler

You should install RepeatMasker and/or RepeatModeler manually if:

  • You do not have the necessary system permissions to install and/or run docker or singularity
  • You need to install a different version of a dependency
  • You need to compile a dependency in a specific way
  • You need to use RepeatMasker as part of another pipeline
  • You need to use AB-BLAST or Cross-Match. Either AB-BLAST or Cross-Match can probably be used with this container, but it is inconvenient and not tested.

Using the Container

Requirements

  • A 64-bit Linux operating system. Other platforms (e.g. macOS) might work with extra effort but are not tested. You will need to have a Linux version of TRF for use inside the container, regardless of the host operating system.
  • singularity or docker installed with permissions to run containers. For docker, this usually means being in the docker group or running the container as the root user.
  • TRF. The license terms of TRF do not allow us to redistribute it inside the container directly, but you can obtain it free of charge from https://tandem.bu.edu/trf/trf.download.html. The container has been tested with TRF 4.09 ("64-bit Linux command line").

Using the Wrapper Script

We provide a wrapper script, dfam-tetools.sh, which does most of the work automatically:

The wrapper script does the following:

  • Runs the container from Docker Hub. This can be overridden with the --container flag if you want to use a different version than the default or if you have a specific .sif file for singularity.
  • Uses singularity if it is available, docker otherwise. You can change this default with --docker or --singularity flags.
  • Makes the host system TRF (found in PATH) available to the container. If necessary, a particular TRF binary can be specified with --trf_prgm=/path/to/trf
  • Runs the container as the current user, in the current working directory
$ curl -sSLO https://github.com/Dfam-consortium/TETools/raw/master/dfam-tetools.sh
$ chmod +x dfam-tetools.sh
$ ./dfam-tetools.sh

Inside the container, the included tools are now available:

$ BuildDatabase -name genome1 genome1.fa
$ RepeatModeler -database genome1 [-LTRStruct] [-pa 8]

$ RepeatMasker genome1.fa [-lib library.fa] [-pa 8]

$ runcoseg.pl -d -m 50 -c ALU.cons -s ALU.seqs -i ALU.ins

Running the Container Manually

The container can also be run manually, bypassing the wrapper script. The only special concern is that TRF must be bind-mounted into the container at /opt/trf:

  • docker run -it --rm --mount type=bind,source=/usr/local/bin/trf,target=/opt/trf,ro dfam/tetools:latest
  • singularity run -B /usr/local/bin/trf:/opt/trf:ro docker://dfam/tetools:latest

Replace /usr/local/bin/trf with the path to trf on your system.

When running the container manually, you will also need to set the UID/GID, directories to mount, and so on according to your specific situation. By default singularity mounts the current directory and your HOME directory; docker does neither.

Using RepBase RepeatMasker Edition

If you wish to use RepBase RepeatMasker Edition with the container, you will need to perform some additional setup. These commands should be read as a container-specific extension to the instructions at http://www.repeatmasker.org/RMDownload.html. These commands assume that RepBaseRepeatMaskerEdition-######.tar.gz is accessible inside the container.

Once inside the container:

# Navigate to an appropriate directory that is persistent outside the container
$ cd /work

# Make a copy of RepeatMasker's Libraries directory here
$ cp -r /opt/RepeatMasker/Libraries/ ./

# Extract RepBase (the .tar.gz file unpacks files into Libraries/)
$ tar -x -f /work/path/to/RepBaseRepeatMaskerEdition-#######.tar.gz

# Run RepeatMasker with the -libdir parameter. RepeatMasker will detect
# the addition of RepBase RepeatMasker Edition and rebuild its cached
# libraries automatically as needed.
$ RepeatMasker -libdir ./Libraries genome.fa

In future runs, you only need the -libdir parameter to specify the path to this same Libraries directory. Each time you update RepeatMasker, remember to also re-create your custom Libraries directory if you use one.

Building the Container

You'll need:

  • curl
  • docker, with permissions to build containers
  • singularity (optional) - if building a singularity container
# Download dependencies
$ ./getsrc.sh

# Build a docker container
$ docker build -t org/name:tag .

# (optional) build a singularity container
$ singularity build dfam-tetools.sif dfam-tetools.def

Included software

The following software is included in the Dfam TE Tools container (version 1.0):

RepeatModeler 2.0 http://www.repeatmasker.org/RepeatModeler/
RepeatMasker 4.1.0 http://www.repeatmasker.org/RMDownload.html
coseg 0.2.2 http://www.repeatmasker.org/COSEGDownload.html
RMBlast 2.9.0-p2 http://www.repeatmasker.org/RMBlast.html
HMMER 3.2.1 http://hmmer.org/
RepeatScout 1.0.6 http://www.repeatmasker.org/RepeatScout-1.0.6.tar.gz
RECON 1.08 http://www.repeatmasker.org/RepeatModeler/RECON-1.08.tar.gz
cd-hit 4.8.1 https://github.com/weizhongli/cdhit
genometools 1.5.10 https://github.com/genometools/genometools
LTR_retriever 2.7 https://github.com/oushujun/LTR_retriever/
MAFFT 7.429 https://mafft.cbrc.jp/alignment/software/
NINJA 0.97-cluster_only https://github.com/TravisWheelerLab/NINJA

License

The Dfam TE Tools container project (the Dockerfile and associated build and run scripts) is licensed under the CC 1.0 Universal Public Domain Dedication. The software packages included in the container have their own associated license terms; see the individual software packages for details.

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