Configuration

SeqUIaSCOPE reads a reference_paths.json file at startup to locate reference files and configure optional features. A default version of this file is embedded in the Docker image. If you need to override any of the defaults — for example to use a custom report template or a custom reference genome — mount your own reference_paths.json into the container.

Mounting a Custom Config

Add the following volume mount to your docker-compose.yaml:

volumes:
  - ./input_files:/input_files:ro
  - ./output_files:/output_files
  - ./reference_paths.json:/srv/shiny-server/sequiaScope/app/reference_paths.json:ro

Place your reference_paths.json in the same directory as the compose file.

Config File Structure

{
  "output_dir": "output_files",
  "reference_files": {
    "kegg_tab": "app/references/kegg_tab.tsv",
    "report_template": "app/references/report_template.docx",
    "genes_of_interest": "app/references/genes_of_interest.tsv"
  },
  "custom_genome": {
    "display_name": "Custom genome",
    "igv_id": "custom",
    "genome": "custom_genome/GRCh38.fa",
    "index": "custom_genome/GRCh38.fa.fai"
  }
}

Configuration Options

`output_dir`

Directory where session data, IGV snapshots, and Arriba reports are stored. Defaults to output_files. In Docker deployments this should match the writable volume mount.

`reference_files`

Paths to the three built-in reference files. All paths are relative to the application root inside the container.

Key	Default	Description
`kegg_tab`	`app/references/kegg_tab.tsv`	KEGG pathway annotation table used by the Network Graph module and expression pathway assignment. Required when using expression or network graph features.
`report_template`	`app/references/report_template.docx`	Default `.docx` template used for report generation in the Summary module. Can be replaced with an institutional template.
`genes_of_interest`	`app/references/genes_of_interest.tsv`	Default genes of interest list used for expression highlighting. See Data Requirements — Genes of Interest for the required file format.

`custom_genome`

Optional section for configuring a custom reference genome for IGV. Remove this section entirely if you are using one of the built-in genomes (GRCh38/hg38, GRCh37/hg19, etc.).

Key	Description
`display_name`	Name shown in the genome picker in the upload form
`igv_id`	Internal identifier — must be set to `"custom"`
`genome`	Path to the FASTA file, relative to the `/input_files` mount
`index`	Path to the FASTA index (`.fai`), relative to the `/input_files` mount

Custom genome files must be placed inside your input_files directory so they are accessible via the /input_files mount. Paths in the config are relative to that mount point.

Summary and Report