Installation¶

Install the Python package¶

pip install refbox

Requires Python ≥ 3.9. The package pulls in pyyaml, requests, tqdm, and pysam.

From source (development)¶

git clone https://github.com/typekey/refbox.git
cd refbox
pip install -e .
pytest -q          # unit tests for `refbox build` single-file modes
refbox --help

External command-line tools¶

refbox shells out to standard bioinformatics tools. Install them once with conda / mamba:

mamba install -c bioconda htslib samtools gffread ucsc-bedtobigbed

Tool	Used for	Required for
`bgzip`	block-gzip compression	every build
`tabix`	positional indexing of GFF/BED	every annotation/BED build
`samtools`	`faidx` on FASTA	genome / transcriptome
`gffread`	extract transcripts from genome + GTF	derived transcriptome
`liftOver`	RNAcentral cross-assembly liftover	assemblies using `liftover_from`
`bedToBigBed` / `bigBedToBed`	bigBed conversion / expansion	`refbox build -bed`, cytoband
GNU `sort`, `grep`	sorting / filtering	every build