ChromHMM
ChromHMM commands download Roadmap dense-state BED files and normalized
metadata. Directly supported species include hg19, hg38, mm39, mm10,
and mm9; other UCSC builds can use liftOver from hg38.
sjcab-peak2anno-db install-chromhmm -m 18 -s hg19 -i E001,E063
sjcab-peak2anno-db download-chromhmm -o chromhmm_downloads -m 25 -s hg19 -c GM12878
sjcab-peak2anno-db download-chromhmm -o chromhmm_downloads -m 18 -s hg38 -i E063
Use --ids/-i, --tissue/-t, and --cellline/-c to select records.
Other UCSC builds use --yes-liftover; chain files are cached under
{db-path}/cache/chains/.
The generated database-level helper is {db-path}/liftover_hg38_to.sh:
bash liftover_hg38_to.sh
bash liftover_hg38_to.sh mm10 crossmap
bash liftover_hg38_to.sh mm10 ucsc
It scans the blacklist, CGI, ChromHMM, and Segway directories and skips files
that already have lifted outputs. CrossMap is the default; auto tries
CrossMap and then UCSC liftOver.
The helper detects package managers in this order: Pixi, micromamba, mamba,
then conda, and installs the required tool when it is unavailable.
Output is stored under {db-path}/chromhmm/{genome} with a metadata.tsv
index.