Segway
Segway downloads the hg19 encyclopedia and can create a liftOver script for
another UCSC assembly. Generated scripts prefer CrossMap and can explicitly
select CrossMap or UCSC liftOver.
sjcab-peak2anno-db install-segway
sjcab-peak2anno-db download-segway -o segway_downloads -i GM12878
sjcab-peak2anno-db download-segway -o segway_downloads -s hg38 --yes-liftover
Lifted files and the helper script are stored under the selected database
directory. The script reuses an existing segway-liftover environment when
available and caches chain files under cache/chains.
Storage layout
With the default database path, Segway files are stored as:
{db-path}/segway/{genome}/segway_encyclopedia.bed.gz
{db-path}/segway/{genome}/caas.bed.gz
{db-path}/segway/{genome}/{sample}.bed.gz
{db-path}/segway/{genome}/metadata.tsv
{db-path}/segway/segway_downloads.tsv
The default {db-path} is ~/.sjcab_peak2anno_db; use --db-path or
SJCAB_PEAK2ANNO_DB_PATH to change it. LiftOver output is written under
{db-path}/segway/{target-genome}/. The shared helper is
{db-path}/liftover_hg38_to.sh; it accepts an optional target and mode, for
example bash liftover_hg38_to.sh mm10 ucsc, and scans all supported resource
folders while skipping existing lifted files.
It detects Pixi, micromamba, mamba, and conda in that order and installs the
required CrossMap or UCSC liftOver package when needed.