generated: '2026-07-19'
method: searched
source: https://docs.gencove.com/base/cli-reference/
name: gencove
binary: gencove
package: packages/gencove-packages.yml
docs: https://docs.gencove.com/base/cli-reference/
install:
- pip install gencove
- conda install -c bioconda gencove
auth:
  env:
  - GENCOVE_API_KEY
  - GENCOVE_EMAIL
  - GENCOVE_PASSWORD
  note: API key and email/password credentials cannot be used simultaneously.
command_groups:
- name: upload
  summary: Submit FASTQ files to Gencove.
- name: uploads
  summary: Track and list upload operations.
- name: download
  summary: Retrieve project deliverables (supports file-type filtering).
- name: projects
  summary: Create, configure and manage projects and their samples.
- name: samples
  summary: Manage sample metadata and file downloads.
- name: basespace
  summary: Manage Illumina BaseSpace imports and biosample operations.
- name: s3
  summary: Manage S3-based imports and auto-imports.
- name: sample-manifests
  summary: Handle sample manifest operations.
- name: explorer
  summary: Access Gencove Explorer data and instance management.
- name: reports
  summary: Generate usage and quality-control reports.
- name: file-types
  summary: Display available file types in the system.
- name: webhooks
  summary: Verify webhook signatures/functionality.
key_flows:
- name: Create a project and analyze samples
  steps:
  - gencove projects create (with a pipeline capability ID)
  - gencove upload
  - gencove projects list-samples
- name: Auto-import from S3
  steps:
  - gencove s3 autoimports
- name: Import from BaseSpace
  steps:
  - gencove basespace projects import
- name: Download deliverables
  steps:
  - gencove download
  - gencove projects get-merged-vcf