refbox 0.1.2

Build standardized, indexed reference files (genome, annotation, repeats, RNAcentral, cCRE) for genome browsers.

refbox

Build standardized, indexed reference files for genome browsers — in one command.

refbox turns a YAML registry of species/assemblies into ready-to-load browser inputs:

• Genome FASTA → bgzip + samtools faidx (.gz + .fai + .gzi)
• Transcriptome FASTA → bgzip + samtools faidx
• GTF / GFF3 annotations → sorted + bgzip + tabix
• Repeats (UCSC RepeatMasker rmsk.txt.gz + .fa.out.gz)
• RNAcentral non-coding RNA annotations
• ENCODE SCREEN cCREs
• chrom.sizes derived from the genome .fai

It ships a registry of 26 species / 42 assemblies (human, mouse, rat, dog, cow, pig, chimp, gorilla, zebrafish, fly, worm, sea urchin, yeast, plants, bacteria, viruses…) covering GENCODE, Ensembl, Ensembl Genomes, UCSC golden path, NCBI, RNAcentral, and ENCODE SCREEN.

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Why

Genome browsers (e.g. WashU Epigenome Browser, rbrowser) expect a strict set of file formats and indices. Manually downloading, sorting, bgzipping, tabixing, and checking each one is tedious and error-prone. refbox makes the process:

• declarative — one YAML, every URL pinned
• idempotent — re-running skips finished files; --force to rebuild
• filterable — --species, --assembly, --resource to scope work
• verifiable — a test subcommand runs real samtools faidx / tabix queries

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Install

pip install refbox

refbox shells out to the standard htslib tooling. Install once via conda/mamba (recommended):

mamba install -c bioconda htslib samtools

Required CLI tools: bgzip, tabix, samtools, GNU sort, grep.

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Quick start

# Download → build → validate Human GRCh38 (uses bundled species.yaml)
refbox download --species Homo_sapiens --assembly GRCh38
refbox build    --species Homo_sapiens --assembly GRCh38
refbox test     --species Homo_sapiens --assembly GRCh38

Or use the one-shot driver:

git clone https://github.com/typekey/refbox.git
cd refbox
./build.sh Homo_sapiens GRCh38

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CLI reference

refbox download [--species ...] [--assembly ...] [--resource ...] [--out DIR] [--force]
refbox build    [--species ...] [--assembly ...] [--resource ...] [--out DIR] [--force]
refbox test     [--species ...] [--assembly ...] [--out DIR]

Flag	Default	Meaning
--species	all enabled	filter to one or more species (e.g. Homo_sapiens)
--assembly	all enabled	filter to one or more assemblies (e.g. GRCh38)
--resource	all 10	subset: genome transcriptome annotation_gtf annotation_gff3 repeats_rmsk repeats_bed repeats_gtf repeats_fa rnacentral ccre
--out	$REFBOX_OUT or $PWD	output root
--force	off	rebuild even when outputs exist
-v / --verbose		enable DEBUG logging

Environment variables:

Name	Meaning
REFBOX_OUT	default output root for {Species}/{Assembly}/{raw,build}/
REFBOX_CONFIG	path to a custom species.yaml (overrides the bundled registry)

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Output layout

{REFBOX_OUT}/
  {Species}/
    {Assembly}/
      raw/                          # original downloads / copies
        genome.fa
        transcriptome.fa
        annotation_gtf.gtf
        annotation_gff3.gff3
        repeats_rmsk.tsv
        repeats_fa.fa
        rnacentral.gff3
        ccre.bed
      build/                        # browser-loadable
        genome.fa.gz                + .fai + .gzi
        chrom.sizes
        transcripts.fa.gz           + .fai
        annotation.sorted.gtf.gz    + .tbi
        annotation.sorted.gff3.gz   + .tbi
        repeats.sorted.bed.gz       + .tbi
        repeats.sorted.gtf.gz       + .tbi
        rnacentral.sorted.gff3.gz   + .tbi
        ccre.sorted.bed.gz          + .tbi

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Examples

1. Build only cCREs for Human GRCh38

refbox download --species Homo_sapiens --assembly GRCh38 --resource ccre
refbox build    --species Homo_sapiens --assembly GRCh38 --resource ccre
refbox test     --species Homo_sapiens --assembly GRCh38

2. Build a full reference into a specific directory

refbox download --species Mus_musculus --assembly GRCm38 --out /data/refs
refbox build    --species Mus_musculus --assembly GRCm38 --out /data/refs
refbox test     --species Mus_musculus --assembly GRCm38 --out /data/refs

3. Use a private YAML registry

export REFBOX_CONFIG=/path/to/my_species.yaml
refbox build

4. Drive everything from build.sh

./build.sh                              # all enabled assemblies
./build.sh Homo_sapiens                 # one species, all enabled assemblies
./build.sh Homo_sapiens GRCh38          # one species + assembly
./build.sh Homo_sapiens GRCh38 -- --resource genome ccre
FORCE=1 ./build.sh Mus_musculus GRCm38  # rebuild even when outputs exist
STEPS="test" ./build.sh                 # only run validation

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Tutorial — adding a new assembly

The registry lives in config/species.yaml. Each entry is three levels deep: species → assembly → resource.

Step 1. Add an assembly block

species:
  Homo_sapiens:
    GRCh38:
      enabled: true                  # set false to keep it idle
      gencode_version: 44
      ucsc_db: hg38

      genome:
        url: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/GRCh38.primary_assembly.genome.fa.gz

      annotation_gtf:
        url: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/gencode.v44.annotation.gtf.gz

      repeats_rmsk:
        url: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/rmsk.txt.gz

      ccre:
        url: https://downloads.wenglab.org/V3/GRCh38-cCREs.bed

Step 2. Each resource entry follows a fallback rule

my_resource:
  local_path: /path/on/disk/file.fa.gz   # used if it exists
  url:        https://.../file.fa.gz     # else downloaded
# omit / null = skipped silently

• local_path exists → copy into raw/ (auto-gunzips .gz)
• otherwise url → download into raw/
• otherwise → skip (no error)

Step 3. Canonical resource names

Name	Output (raw)	Output (build)
genome	genome.fa	genome.fa.gz + .fai + .gzi, chrom.sizes
transcriptome	transcriptome.fa	transcripts.fa.gz + .fai
annotation_gtf	annotation_gtf.gtf	annotation.sorted.gtf.gz + .tbi
annotation_gff3	annotation_gff3.gff3	annotation.sorted.gff3.gz + .tbi
repeats_rmsk	repeats_rmsk.tsv	(raw input for repeats_bed/gtf — derivation TODO)
repeats_bed	repeats_bed.bed	repeats.sorted.bed.gz + .tbi
repeats_gtf	repeats_gtf.gtf	repeats.sorted.gtf.gz + .tbi
repeats_fa	repeats_fa.fa	(RepeatMasker .fa.out report)
rnacentral	rnacentral.gff3	rnacentral.sorted.gff3.gz + .tbi
ccre	ccre.bed	ccre.sorted.bed.gz + .tbi

Step 4. Run

refbox download --species Homo_sapiens --assembly GRCh38
refbox build    --species Homo_sapiens --assembly GRCh38
refbox test     --species Homo_sapiens --assembly GRCh38

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Programmatic API

from refbox.config import load_config, iter_targets
from refbox.download import download_targets
from refbox.build import build_targets
from refbox.test import test_targets

cfg = load_config()
for t in iter_targets(cfg, species=["Homo_sapiens"]):
    print(t.species, t.assembly, list(t.resources))

download_targets(species=["Homo_sapiens"], assembly=["GRCh38"], out="/data/refs")
build_targets(   species=["Homo_sapiens"], assembly=["GRCh38"], out="/data/refs")
test_targets(    species=["Homo_sapiens"], assembly=["GRCh38"], out="/data/refs")

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Development

git clone https://github.com/typekey/refbox.git
cd refbox
pip install -e .
refbox --help

Release

Tags matching v* automatically build and publish to PyPI via GitHub Actions (.github/workflows/workflow.yml) using PyPI trusted publishing (no API token required).

git tag v0.1.0
git push origin v0.1.0

Manual build (no upload):

./release.sh build       # writes dist/

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License

MIT — see LICENSE.