Quick Start¶

1. Build a configured assembly end-to-end¶

The registry-driven pipeline (pull) does download → build → test → publish in one shot, using the bundled species.yaml:

# Fetch + build + validate + publish Human GRCh38
refbox pull --species Homo_sapiens --assembly GRCh38

# --species is optional; it is inferred from --assembly
refbox pull --assembly GRCm38

Outputs land under $REFBOX_OUT/<Species>/<Assembly>/ as flattened <Assembly>.<name> files (e.g. GRCh38.genome.fa.gz). See Output Layout.

2. Build a single arbitrary file¶

No species.yaml entry needed — bring your own data:

# Genome FASTA → bgzip + faidx + chrom.sizes
refbox build -fa my_genome.fa

# GTF/GFF3 → sorted + bgzip + tabix
refbox build -gtf my_annotation.gtf

# BED → sorted + bgzip + tabix + bigBed
refbox build -bed peaks.bed --assembly GRCh38

See the full Build Command reference.

3. Build a search index (the question everyone asks)¶

Full index (.rba)Lite index (.rbi)

# Standalone RBrowser Index (SQLite + FTS5 search)
refbox build -rba gencode.v45.annotation.gtf.gz -o hg38.gencode.v45.rba \
    --source-name GENCODE --species human --genome hg38 \
    --annotation-version v45 --force

Or emit it alongside the tabix output in one command:

refbox build -gtf gencode.v45.annotation.gtf.gz --with-rba \
    --source-name GENCODE --genome hg38 --annotation-version v45

Details → RBrowser Index .rba.

refbox build -rbi gencode.v45.annotation.gtf.gz -o hg38.gencode.v45.rbi \
    --source-name GENCODE --species human --genome hg38 \
    --annotation-version v45 --force

Details → Lite Index .rbi.

4. The one-shot driver script¶

build.sh wraps refbox pull with sensible defaults (output root = repo parent):

./build.sh                            # all enabled assemblies
./build.sh Homo_sapiens               # one species (all enabled assemblies)
./build.sh Homo_sapiens GRCh38        # one species + assembly
./build.sh -- --resource genome cytoband   # extra args after `--` go to refbox

# environment toggles
FORCE=1 ./build.sh Homo_sapiens GRCh38     # re-download + rebuild
NO_TEST=1 ./build.sh                       # skip validation
INCLUDE_DISABLED=1 ./build.sh              # also process enabled: false entries