Dfam TE Tools Container

Note that as of version 1.88 TETools contains RepeatMasker 4.1.6. This version of RepeatMasker uses a new version of FamDB with a new format. This README contains instructions for modifying the files available to the TETools container, but the README file in the FamDB repository contains more information on the format itself.

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, or appropriate virtualization software. Docker for Mac is known to work, including the wrapper script, but we do not regularly test this platform ourselves.
• 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. You can also use the --container option to specify a different version of the container or an .sif file for singularity.
• Uses singularity if it is available, or docker. You can choose between them with the --docker or --singularity options.
• Runs the container as the current user, with the current working directory accessible from within the container. Depending on the environment and the software used, this directory appears inside the container at its original location and/or at the path /work.
• Binds a directory, ideally named Libraries, into the container over /opt/RepeatMasker/Libraries with the --library option. This is intended to enable the modification of local FamDB files, as the container is packaged with a minimal FamDB file. Note that this will overwrite the library files within the container. To avoid this, copy those files to the host system using the steps below under Customizing the RepeatMasker libraries.

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] [-threads 16]

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 needs. By default singularity mounts the current directory and your HOME directory; docker does neither.

You can also use singularity pull to download the container to a file:

singularity pull dfam-tetools-latest.sif docker://dfam/tetools:latest
singularity run dfam-tetools-latest.sif

Customizing the RepeatMasker libraries

Currently, RepeatMasker is installed without a TE library, however it will support annotation with custom libraries (using the -lib mylib.fa command line option).

Additional setup is necesary to use TE libraries such as Dfam or RepBase for use with the container. Modifying the container can become a quite complex task, depending on which software and versions are being used and how the system is configured. Instead these instructions will create a modifiable local Libraries folder that can be mounted back into the container.

The first step is to copy the RepeatMasker Libraries out of the container to the host filesystem:

# Enter the container tagged with <tag>. This command will also mount your current directory to 
# /work inside the container
docker run -it --rm --workdir /work -v $(pwd):/work dfam/tetools:<tag>

# confirm visibility to your working directory
ls

# Make a copy of the original RepeatMasker Libraries/ directory on your host filesystem
cp -r /opt/RepeatMasker/Libraries/ ./

# exit the container
exit

# Make sure you own the Libraries folder
chown -R $USER ./Libraries/

# Remove the minimal famdb files
rm ./Libraries/famdb/*

To include Dfam you will need to download one or more famdb partitions from the Dfam site. The top level partition ( partition 0 ) will be necessary, however additional partitions are optional. The contens of the partitions for the current release can be found here FamDB README. The partitions may be downloaded from here Dfam.org.

To include the Dfam FamDB files, download, unzip, and include them in Libraries/famdb. They will be detected and included in queries automatically.

Whenever you modify the FamDB files, the RepeatMasker libraries must be regenerated.

# run the container binding your host Libraries directory over the RepeatMasker directory
docker run -it --rm -v <host path>/Libraries:/opt/RepeatMasker/Libraries dfam/tetools:<tag>

# navigate to the RepeatMasker folder
cd /opt/RepeatMasker

# unlock libaries for reconfiguring 
rm ./Libraries/famdb/rmlib.config

# run the reconfigure script
./tetoolsDfamUpdate.pl

To include RepBase data, download and unzip RepBaseRepeatMaskerEdition-#######.tar.gz into Libraries and run the updater script.

# Unpack the RepBase data
tar -xvzf /work/path/to/Libaries/RepBaseRepeatMaskerEdition-#######.tar.gz

# run the container. You can also use the first command above again
./dfam-tetools.sh --docker

# navigate to the RepeatMasker folder
cd /opt/RepeatMasker

# unlock libaries for reconfiguring 
rm ./Libraries/famdb/rmlib.config

# rerun the reconfigure script
./tetoolsDfamUpdate.pl

When using the image with the new Libraries folder, mount it to the container using the -v argument. All paths must be absolute. ./dfam-tetools.sh does this automatically.

-v <host filesystem path to Libraries>/Libraries:/opt/RepeatMasker/Libraries

Note that the process for modifying the files in a Singularity container is identical, but the arguments vary slightly. For example, instead of -v Singularity uses -B. dfam-tetools.sh also does not currently automatically mount host library directories for Singularity.

You can now specify this `Libraries/` directory by setting the `LIBDIR` environment variable, for example with the `export LIBDIR=` command or `-e LIBDIR=` depending on you are running the container.

When you use a new version of the TETools container (particularly a new RepeatMasker), you should re-create the Libraries directory for the new version.

# Set the LIBDIR environment variable before running RepeatMasker
export LIBDIR=/path/to/Libraries
RepeatMasker genome.fa

Building the Container

You will 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

Multi-Platform Docker Build

docker buildx build --platform=linux/amd64,linux/arm64 --output=type=registry -t dfam/tetools:<tag> .

Included software

The following software is included in the Dfam TE Tools container (version 1.90):

RepeatModeler	2.0.6	https://github.com/Dfam-consortium/RepeatModeler
RepeatMasker	4.1.7-p1	http://www.repeatmasker.org/RMDownload.html
coseg	0.2.3	http://www.repeatmasker.org/COSEGDownload.html
RMBlast	2.14.1	http://www.repeatmasker.org/RMBlast.html
HMMER	3.4	http://hmmer.org/
TRF	4.09.1	https://github.com/Benson-Genomics-Lab/TRF
RepeatScout	1.0.7	https://github.com/Dfam-consortium/RepeatScout
RECON	1.08	http://www.repeatmasker.org/RepeatModeler/RECON-1.08.tar.gz
cd-hit	4.8.1	https://github.com/weizhongli/cdhit
genometools	1.6.4	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	1.00-cluster_only	https://github.com/TravisWheelerLab/NINJA
UCSC utilities*	v413	http://hgdownload.soe.ucsc.edu/admin/exe/>

* Selected tools only: faToTwoBit, twoBitInfo, twoBitToFa

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.