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InstallationInfrastructure JSON

Infrastructure JSON

Create a file named infrastructure-setup.json to pre-configure your environment. In interactive mode, the installer asks for these values one by one. The config file lets you skip prompts and automate setup.

For a lightweight first install, start with:

{
  "port": 8000,
  "pipelinesEnabled": false
}

For full infrastructure control, use a complete config template:

{
  "port": 8000,
  "pipelinesEnabled": true,
  "nextAuthUrl": "http://seqdesk-host:8000",
  "databaseUrl": "postgresql://seqdesk:replace-with-password@127.0.0.1:5432/seqdesk?schema=public",
  "directUrl": "postgresql://seqdesk:replace-with-password@127.0.0.1:5432/seqdesk?schema=public",
  "anthropicApiKey": "replace-with-anthropic-api-key",
  "sequencingDataDir": "/data/sequencing",
  "pipelineRunDir": "/data/pipeline_runs",
  "useSlurm": true,
  "slurmQueue": "cpu",
  "slurmCores": 4,
  "slurmMemory": "64GB",
  "slurmTimeLimit": 12,
  "slurmOptions": "--qos=standard",
  "condaPath": "/opt/miniconda3",
  "condaEnv": "seqdesk-pipelines",
  "nextflowProfile": "conda",
  "nextflowWeblogUrl": "http://seqdesk-host:8000/api/pipelines/weblog",
  "weblogSecret": "replace-with-random-secret",
  "privatePipelines": {
    "metaxpath": {
      "packageUrl": "https://www.seqdesk.com/api/private/metaxpath/0.1.0",
      "key": "replace-with-metaxpath-key",
      "sha256": "78a9d569af34dac31fd825e9ee4b1ab79f839de0708fd4ec47144af73871808a"
    }
  }
}

Use placeholder values in any file you share publicly.

Field reference

Core

  • port: HTTP port SeqDesk listens on.
  • pipelinesEnabled: Set to false to skip pipeline setup during install.
  • nextAuthUrl: Public base URL used for authentication callbacks.
  • databaseUrl: PostgreSQL runtime connection string.
  • directUrl: Optional direct PostgreSQL connection for Prisma migrations. When omitted, SeqDesk uses databaseUrl.
  • anthropicApiKey: Optional Anthropic API key for AI validation features.

Storage and runtime

  • sequencingDataDir: Root directory containing raw sequencing run folders.
  • pipelineRunDir: Directory for pipeline execution output and work files.
  • useSlurm: Enable Slurm job submission; when false, pipelines run locally.
  • slurmQueue: Slurm partition/queue.
  • slurmCores: CPU cores requested per Slurm job.
  • slurmMemory: Memory per Slurm job (for example "64GB").
  • slurmTimeLimit: Maximum wall-clock hours per Slurm job.
  • slurmOptions: Extra sbatch flags (QOS, account, etc.).

Conda and Nextflow

  • condaPath: Path to Conda/Miniconda used by pipelines.
  • condaEnv: Conda environment name for SeqDesk pipeline dependencies.
  • nextflowProfile: Nextflow profile (conda, docker, singularity).
  • nextflowWeblogUrl: Endpoint where Nextflow sends run progress events.
  • weblogSecret: Shared secret used to authenticate weblog requests.

Private pipeline package

  • privatePipelines.metaxpath.packageUrl: Private tarball URL for MetaxPath.
  • privatePipelines.metaxpath.key: Bearer token used to download the private package.
  • privatePipelines.metaxpath.sha256: Optional tarball checksum for integrity verification.

Configure later in app

  • Admin > Data Storage: Set sequencing data base path.
  • Admin > Pipeline Runtime: Configure run directory, Slurm/local mode, Conda and Nextflow settings.
  • Private MetaxPath install: Installer attempts private package install only when both privatePipelines.metaxpath.packageUrl and privatePipelines.metaxpath.key are set.
  • Reconfigure from JSON: Edit infrastructure-setup.json and re-run installer with --reconfigure.