Settings and config

Open Settings from the top-left menu. Settings save automatically; a status message at the bottom reports any save failure.

The config file is .gw.ini, usually in your home directory or under ~/.config. You can edit it by hand — delete it and GW creates a fresh one on restart.

Settings sections can also be opened as commands: settings, general, genomes, interaction, labelling, navigation, tracks, thresholds, keymap.

Screenshot placeholder — settings dialog with the theme editor
docs/assets/images/v2/settings.png

Reference genomes

A reference genome is a unique genome-tag (e.g. hg19, t2t) plus a local or online FASTA path. Always use a local file for best performance. Genomes can be selected in three ways:

Startup picker — when GW starts without a reference, a terminal (ncurses) picker lists the online genomes. Type a number or a tag such as hg38.
ImGui menus — Settings → Genomes (+, tag, path), or the online files dialog.
Config file — the [genomes] section of .gw.ini, or load genome hg38 in the command box.

Custom themes and color palettes

Open the custom theme settings and enable Use custom colors. Create your own color palettes: select a saved theme, or enter a Name and click New/Duplicate. Each theme has an igv, dark or slate base. Saved themes appear in Settings → General and via the theme <name> command (names can contain spaces).

Click a swatch to open the colour picker and build a palette — backgrounds, reads, nucleotides, coverage, tracks, text, highlights, base modifications and translation colors are all adjustable. A live preview updates as you edit.

Themes live in .gw.theme.json beside .gw.ini, using gwplot palette names and [alpha, red, green, blue] arrays (0–255); only overridden colours are saved:

{
  "version": 1,
  "themes": [
    {"name": "Ocean", "base": "dark", "colors": {"BACKGROUND": [255, 20, 30, 45]}}
  ]
}

Copy the JSON to share themes; Reload JSON reads external changes. Legacy gwplot colour maps load as a theme called Custom.

Default tracks

Default tracks (loaded automatically at startup) are set in Settings → Tracks.