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Third-party software and data

The ORACLE workflow code in this repository is licensed under the MIT License. The workflow installs and invokes separate third-party packages through Conda/Bioconda; it does not relicense those packages. Reference genomes, annotations, blacklists, and motif databases also retain their source-specific terms.

This file is a practical inventory, not legal advice. Users distributing an environment, container, reference bundle, or derived database should review the exact package build and upstream terms themselves.

Main command-line packages

The license labels below follow the metadata of the declared Conda/Bioconda packages used by the workflow at the time this file was reviewed. Environment specifications pin or constrain compatibility-sensitive tools; they are not immutable lock files.

Package Workflow role Package metadata license
fastp read trimming and QC MIT
FastQC raw-read QC GPL-3.0-or-later
MultiQC combined report GPL-3.0-or-later
Bowtie2 paired-end alignment GPL-3.0-or-later
SAMtools BAM processing MIT
Picard duplicate marking and metrics MIT
deepTools Tn5 shifting, coverage, and QC plots MIT
MACS3 peak calling BSD-3-Clause
Genrich optional condition-level peak cross-check MIT
Subread/featureCounts peak quantification GPL-3.0-only
SRA Toolkit SRA download and conversion Public Domain in package metadata; review bundled notices
HOMER 4.11 motif enrichment GNU GPL v3 in the Bioconda package metadata

HOMER is installed from the pinned Bioconda package and receives the configured FASTA directly. The workflow does not install or redistribute HOMER genome packages. If a different HOMER build or auxiliary dataset is used, review that build's metadata and data terms separately.

The optional TOBIAS environment and all transitive dependencies retain their own licenses. Inspect the resolved Conda package metadata for the exact build used in a run.

R, Bioconductor, and Python packages

DESeq2, ashr, ChIPseeker, clusterProfiler, chromVAR, JASPAR2020, genome annotation packages, pandas, pysam, plotting libraries, Snakemake, and their dependencies are installed as separate packages. Their licenses are not uniform. The authoritative record for a particular run is the resolved package metadata plus each upstream project's license.

JASPAR and other motif databases

JASPAR CORE data are provided under CC BY 4.0 and require attribution. This applies to JASPAR motif data independently of the license of the R package or software used to read them.

TOBIAS accepts user-supplied motif databases. A file's syntax does not determine its license: a motif file in MEME format does not acquire the MEME Suite software license merely because it uses that format. Cite and follow the terms of the database from which the motifs were obtained. The workflow does not run the MEME Suite.

Reference genomes, annotations, and blacklists

Reference data are downloaded or supplied by the user and are not covered by this repository's MIT license. Record and review the terms for the exact versions used, including:

  • Ensembl or another FASTA/GTF provider;
  • the Boyle Lab/ENCODE blacklist source;
  • TxDb, OrgDb, BSgenome, and related annotation data;
  • JASPAR or another motif collection;
  • GO and KEGG resources used for enrichment.

Do not assume that a data resource is unrestricted because it can be downloaded automatically. Preserve required attribution and any version-specific notices with the analysis provenance.