repeatmasker

TAFFISH app for RepeatMasker, a widely used tool for screening DNA sequences for interspersed repeats and low-complexity DNA.

Package Identity

• name: repeatmasker
• command: taf-repeatmasker
• version: 4.2.3-r3
• kind: tool
• image: ghcr.io/taffish/repeatmasker:4.2.3-r3
• upstream: RepeatMasker 4.2.3
• runtime version: RepeatMasker version 4.2.3
• default command: RepeatMasker
• default search engine: rmblast
• native platform: linux/amd64

The image is configured non-interactively with RMBlast, TRF, HMMER, and small UCSC helper tools used by RepeatMasker utilities. PAGER=cat is set so upstream RepeatMasker help prints and exits instead of entering more. The app is intended for offline custom-library runs and for Dfam/FamDB runs when users provide the required database partitions.

Install

taf install repeatmasker

Usage

TAFFISH wrapper help:

taf-repeatmasker --help
taf-repeatmasker --version
taf-repeatmasker --compile

Upstream RepeatMasker help and version:

taf-repeatmasker -- -help
taf-repeatmasker -- --help
taf-repeatmasker -- -v
taf-repeatmasker RepeatMasker -v

Run with a custom repeat library:

taf-repeatmasker -pa 8 -engine rmblast -lib repeats.fa -dir rm-out genome.fa

Run bundled utility commands through command mode:

taf-repeatmasker famdb.py -i /opt/RepeatMasker/Libraries/famdb info
taf-repeatmasker rmOutToGFF3.pl genome.fa.out > genome.fa.out.gff
taf-repeatmasker buildSummary.pl genome.fa.out > genome.fa.tbl
taf-repeatmasker rmToTrackHub.pl -out genome.fa.out -genome hg38
taf-repeatmasker rmblastn -version
taf-repeatmasker trf -v

Wrapper Semantics

taf-repeatmasker defaults to the upstream RepeatMasker command. Because RepeatMasker uses single-dash options such as -pa, -lib, -species, and -dir, normal option-led calls are passed directly to RepeatMasker.

Command mode remains enabled. If the first argument is another executable name, TAFFISH runs that command in the same configured container:

taf-repeatmasker famdb.py --help
taf-repeatmasker ProcessRepeats -help
taf-repeatmasker rmblastn -version

Runtime Contents

The image installs the official RepeatMasker-4.2.3.tar.gz release, copies RMBlast from the ghcr.io/taffish/rmblast:2.17.1-r1 app image, and installs pinned UCSC command-line helper binaries needed by RepeatMasker utility scripts. The Dockerfile verifies the RepeatMasker and UCSC helper checksums:

RepeatMasker-4.2.3.tar.gz
832e2b22aef6763ef7d5dd2771eef22f7dd8b9738bea0e1d81295aa511b61e6a

twoBitInfo
fca5427e1aedd00be0d32117420010c9162d442562c83305b2d3e3c8e6cebe71

bedToBigBed
73e10feef3a685304d71c840058ae9a5113bdc4e134f161d3913cfebc5a2ec24

The RMBlast source checksum is enforced by the separate rmblast taf-app:

rmblast-2.17.1+-x64-linux.tar.gz
9ddf0ffdc01f3dd7bf62bbcb01516757b1e732e54674e81d93a7c143157aa527

Packaged RepeatMasker commands and utilities include:

• RepeatMasker
• ProcessRepeats
• RepeatProteinMask
• DupMasker
• famdb.py
• RM2Bed.py
• rmOutToGFF3.pl
• buildSummary.pl
• calcDivergenceFromAlign.pl
• createRepeatLandscape.pl
• rmToTrackHub.pl
• maskFile.pl
• buildRMLibFromEMBL.pl

Search/runtime tools include:

• RMBlast 2.17.1+ (rmblastn, makeblastdb, and companion BLAST+ tools)
• TRF 4.09.1 from Debian
• HMMER 3.3.2 from Debian
• UCSC twoBitInfo and bedToBigBed helper binaries
• Perl, Python 3, Python h5py, curl, gzip, tar, and required shared libraries

BLAST_USAGE_REPORT=false is set by default so RMBlast does not report usage statistics during local TAFFISH runs. PAGER=cat is set by default so RepeatMasker help remains non-interactive and works predictably in terminals, pipelines, CI, and TAFFISH flow contexts.

Libraries And Data

The official RepeatMasker 4.2.3 tarball includes the Dfam 3.9 root FamDB partition:

/opt/RepeatMasker/Libraries/famdb/dfam39_full.0.h5

This root partition is required metadata and contains a small set of root-level families. It is not the full Dfam database. Full species or clade coverage requires adding matching Dfam 3.9 FamDB partitions under /opt/RepeatMasker/Libraries/famdb, or using -lib with a custom FASTA repeat library.

RepBase is not included. RepBase RepeatMasker Edition and later RepBase data must be obtained by users under their own authorization and used according to their license terms.

Platform

This app is native linux/amd64 only because it uses the official RMBlast x64 Linux binary. src/main.taf asks Docker and Podman to run with --platform linux/amd64. On arm64 hosts this is amd64 emulation, not native arm64 support. Apptainer behavior depends on the host's ability to run amd64 containers.

Boundaries

This core image does not include:

• full Dfam partitions beyond the root partition included upstream
• RepBase
• cross_match
• ABBLAST/WUBlast
• a from-source RMBlast build inside this Dockerfile; it depends on the ghcr.io/taffish/rmblast:2.17.1-r1 app image at build time
• Entrez Direct or online database download workflows, except utility scripts such as rmToTrackHub.pl can still use curl to fetch UCSC chromosome sizes when users request those workflows

The smoke tests validate the configured program stack and small offline functional runs. They do not substitute for full biological validation on large genomes or species-specific repeat libraries.

License Boundary

The TAFFISH app packaging files are licensed under Apache-2.0. The packaged upstream RepeatMasker software is covered by: OSL-2.1 with bundled Dfam/FamDB CC0 code/data notices, RMBlast/NCBI components, and UCSC command-line utilities. Bundled third-party components, datasets, models, and external resources keep their own license terms.

License And Citation

RepeatMasker open-4.0 and later are distributed under the Open Software License v2.1. The bundled FamDB code is documented by upstream as CC0. RMBlast and NCBI BLAST+ notices are included through the RMBlast distribution. UCSC twoBitInfo and bedToBigBed are included as command-line utilities for RepeatMasker helper-script compatibility; consult the UCSC Genome Browser/Kent source terms for those tools.

Please refer to:

• Smit, AFA, Hubley, R. & Green, P. RepeatMasker at https://www.repeatmasker.org/
• Dfam Consortium for Dfam/FamDB data
• Camacho et al. 2009 for BLAST+. DOI: 10.1186/1471-2105-10-421; PMID: 20003500

Smoke Coverage

Smoke tests cover:

• RepeatMasker, RMBlast, TRF, HMMER, and usage-reporting version/state checks.
• RepeatMasker non-interactive --help and ProcessRepeats help.
• FamDB info for the included Dfam 3.9 root partition.
• RepeatMasker configuration paths for RMBlast, TRF, HMMER, and default engine.
• A tiny offline RepeatMasker -lib run producing .out and .masked.
• A tiny offline RepeatMasker -gff -lib run producing .out.gff.
• Utility conversion/summary scripts on a tiny real RepeatMasker .out file, including the UCSC twoBitInfo helper required by buildSummary.pl.