dfam/tetools repository overview

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.

The easiest and recommended way to use this container is through a wrapper script we develop alongside it. Further details are available at https://github.com/Dfam-consortium/TETools/⁠.