Command-line reference

Run tracknado --help or tracknado <command> --help to see the options installed with your version.

tracknado design

Create an editable CSV from track files. It writes one row per input with file_path, name, and ext, plus empty color, supertrack, composite, and overlay columns.

tracknado design -i tracks/*.bw -o tracks.csv

Option	Meaning
-i, --input-files	One or more track files or glob patterns (for example, 'tracks/*.bw'). Repeat the option to add another set. Quote glob patterns to let TrackNado expand them, including recursive ** patterns.
-o, --output	CSV or TSV path to write.
--seqnado	Extract fields from a seqnado-style directory layout.
--grouping-regex	Extract named groups from file names.

tracknado create

Build and stage a hub from either a metadata table or input files.

tracknado create --metadata tracks.csv --output my_hub --genome-name hg38

Option	Meaning
-i, --input-files	Track files or glob patterns to include. Quote patterns such as 'tracks/**/*.bigWig' to let TrackNado expand them. Use this instead of --metadata when no table is needed.
-m, --metadata	CSV or TSV with a file_path column.
-o, --output	Staged hub directory. Required unless creating a template.
-t, --template	Write a header-only metadata template and exit.
--hub-name	Short hub identifier; used in the .hub.txt filename.
--hub-email	Contact email stored in the hub.
--genome-name	Genome assembly identifier, such as hg38 or mm10.
--supergroup-by	Metadata field(s) for top-level supertracks.
--subgroup-by	Metadata field(s) for composite-track dimensions.
--overlay-by	Metadata field(s) for overlay tracks.
--color-by	Metadata field used to assign colours.
--seqnado	Extract metadata from a seqnado-style path.
--grouping-regex	Extract named metadata fields from file names.
--convert	Convert BED and GTF/GFF inputs to UCSC formats.
--chrom-sizes	Required alongside --convert; sizes for the target assembly.
--custom-genome	Build an assembly hub. Requires --twobit and --organism.
--twobit	Sequence file for a custom assembly.
--organism	Common organism name for a custom assembly.
--default-pos	Initial custom-assembly browser position.
--description	HTML file to include as the hub landing page.
--sort-metadata	Sort non-standard metadata columns in the saved configuration.
--remove-existing	Remove the existing output directory before staging.
--hosting	Name of a user-defined TOML hosting profile used to report the public hub URL.
--hosting-config	Optional path to the TOML hosting-profile file. Defaults to ~/.config/tracknado/hosting.toml (or $XDG_CONFIG_HOME/tracknado/hosting.toml).
--hub-url-file	Write the resolved public hub URL to a text file. Requires --hosting.

tracknado merge

Create one hub from the tracknado_config.json files produced by earlier builds:

tracknado merge a/tracknado_config.json b/tracknado_config.json --output merged_hub

Use --hub-name, --genome-name, and --hub-email to set the merged hub metadata. --sort-metadata and --remove-existing have the same meaning as for create.

tracknado validate

Check a staged hub directory or a .hub.txt file:

tracknado validate my_hub --strict

--strict treats warnings as errors.