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.
• 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.

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.
• 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:

• docker run -it --rm dfam/tetools:latest
• singularity run docker://dfam/tetools:latest

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 the 'addRepBase.pl' script (part of the RepeatMasker package) to merge the databases,
# specifying the custom Libraries directory.
$ addRepBase.pl -libdir Libraries/

# Run RepeatMasker with the LIBDIR environment variable set
$ export LIBDIR=/path/to/Libraries
$ RepeatMasker genome.fa

In future runs you can reuse the same Libraries/ directory by setting LIBDIR again. Each time you update RepeatMasker, including a new version of the TETools container, you should 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 1.2):

RepeatModeler	2.0.1	http://www.repeatmasker.org/RepeatModeler/
RepeatMasker	4.1.1	http://www.repeatmasker.org/RMDownload.html
coseg	0.2.2	http://www.repeatmasker.org/COSEGDownload.html
RMBlast	2.10.0	http://www.repeatmasker.org/RMBlast.html
HMMER	3.3	http://hmmer.org/
TRF	4.09.1	https://github.com/Benson-Genomics-Lab/TRF
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	1.6.0	https://github.com/genometools/genometools
LTR_retriever	2.9.0	https://github.com/oushujun/LTR_retriever/
MAFFT	7.471	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.