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
.
NOTE: When using the wrapper script with the --docker
option, it will attempt to mount the host $(pwd)/Libraries
folder to the container /opt/RepeatMasker/Libraries
folder. This is intended to enable the modification of local FamDB files, but it will also 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
By default, RepeatMasker is only packaged with the root (0th) FamDB file. Details about
the contents of the files are available from the [FamDB repo](https://github.com/Dfam-consortium/FamDB)
and the files themselves are available to download from [Dfam.org](https://www.dfam.org/releases/Dfam_3.8/families/FamDB/)
Additional setup is needed to install additional FamDB files and/or to install
RepBase RepeatMasker Edition for use with the container. This is a different
process from using a custom library of FASTA or HMM models, which can be
accomplished by using the `-lib` option to `RepeatMasker`.
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:
```sh
# Enter the container tagged with
. This command will also mount your current directory to
# /work inside the container
docker run -it --rm --workdir /work -v $(pwd):/work dfam/tetools:
# 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/
```
To include additional FamDB files, download, unzip, and include them in `Libraries/famdb`.
They will be detected and included in queries automatically. Note that you will need a copy of the 0th partition in the host `Libraries` folder in addition to any addtitional files. It should be copied out of the container with above steps.
Whenever you modify the FamDB files, the RepeatMasker libraries must be regenerated.
```sh
# run the container binding your host Libraries directory over the RepeatMasker directory
docker run -it --rm -v /Libraries:/opt/RepeatMasker/Libraries dfam/tetools:
# 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.
```sh
# 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 /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.
```sh
# 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
```sh
# 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: .
```
## Included software
The following software is included in the Dfam TE Tools container (version `1.88.5`):
| | | |
| -------------- | -------- | --- |
| RepeatModeler | 2.0.5 |
| RepeatMasker | 4.1.6 |
| coseg | 0.2.3 |
| | | |
| RMBlast | 2.14.1 |
| HMMER | 3.4 |
| TRF | 4.09.1 | |
| RepeatScout | 1.0.6 |
| RECON | 1.08 |
| cd-hit | 4.8.1 |
| genometools | 1.6.4 |
| LTR\_retriever | 2.9.0 |
| MAFFT | 7.471 |
| NINJA | 0.99-cluster\_only |
| UCSC utilities\* | v413 | >
\* 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.