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Welcome to Gencove's CLI documentation!

Python library which enables you to use Gencoves' research backend.

Supported Python versions are 3.6 and above.

Quickstart

Installation

To check your default Python version, open an interactive shell and run:

python --version

To check if you have Python 3, open an interactive shell and run:

python3 --version

To install Gencove CLI Tool, open an interactive shell and run:

python<version> -m pip install gencove

If you want Gencove CLI Tool to be installed for your default Python installation, you can instead use:

python -m pip install gencove

Using Gencove CLI Tool

To start using Gencove CLI Tool, open an interactive shell and run:

gencove --help

This will output all available commands.

gencove

Gencove's command line interface.

Usage:

gencove [OPTIONS] COMMAND [ARGS]...

Options:

  --version  Show the version and exit.
  --help     Show this message and exit.

Subcommands

  • basespace: BaseSpace managements commands.
  • download: Download deliverables of a project.
  • explorer: Gencove Explorer commands.
  • file-types: List file types in Gencove's system.
  • projects: Project managements commands.
  • reports: Report management commands.
  • s3: S3 imports managements commands.
  • sample-manifests: Sample manifest management commands.
  • samples: Sample managements commands.
  • upload: Upload FASTQ files to Gencove's system.
  • uploads: Uploads management commands.
  • webhooks: Webhook managements commands.

gencove basespace

BaseSpace managements commands.

Usage:

gencove basespace [OPTIONS] COMMAND [ARGS]...

Options:

  --help  Show this message and exit.

Subcommands

  • autoimports: BaseSpace autoimports management commands.
  • biosamples: BaseSpace Biosamples management commands.
  • projects: BaseSpace projects management commands.

gencove basespace autoimports

BaseSpace autoimports management commands.

Usage:

gencove basespace autoimports [OPTIONS] COMMAND [ARGS]...

Options:

  --help  Show this message and exit.

Subcommands

  • create: Sets up periodic import of BaseSpace projects (their Biosamples) whose name contain the identifer
  • list: Lists periodic import of BaseSpace projects (their Biosamples) jobs.

gencove basespace autoimports create

Sets up periodic import of BaseSpace projects (their Biosamples) whose name contain the identifer to a project in Gencove. Optionally assign metadata to the samples to be added when the automatic import job runs.

PROJECT_ID: Gencove project ID

IDENTIFIER: string used for identifying projects on BaseSpace

Examples:

Set up automatic import of BaseSpace projects' samples that contain the identifier to a project:

    gencove basespace autoimports create 06a5d04b-526a-4471-83ba-fb54e0941758 identifier-in-basespace-project-name

Set up automatic import of BaseSpace projects' samples that contain the identifier to a project with metadata:

    gencove basespace autoimports create 06a5d04b-526a-4471-83ba-fb54e0941758 identifier-in-basespace-project-name --metadata-json='{"batch": "batch1"}'

Usage:

gencove basespace autoimports create [OPTIONS] PROJECT_ID IDENTIFIER

Options:

  --metadata-json TEXT  Add metadata to all samples that are to be imported
                        from BaseSpace to a project.
  --host TEXT           Optional Gencove API host, including http/s protocol.
                        Can be passed as GENCOVE_HOST environment variable.
                        Defaults to https://api.gencove.com
  --email TEXT          Gencove user email to be used in login. Can be passed
                        as GENCOVE_EMAIL environment variable.
  --password TEXT       Gencove user password to be used in login. Can be
                        passed as GENCOVE_PASSWORD environment variable. When
                        MFA is configured, an MFA token will have to be
                        provided after the command is executed.
  --api-key TEXT        Gencove api key. Can be passed as GENCOVE_API_KEY
                        environment variable. When using the API key, an MFA
                        token does not need to be provided.
  --help                Show this message and exit.

gencove basespace autoimports list

Lists periodic import of BaseSpace projects (their Biosamples) jobs.

Examples:

List automatic import jobs of BaseSpace projects:

    gencove basespace autoimports list

Usage:

gencove basespace autoimports list [OPTIONS]

Options:

  --host TEXT      Optional Gencove API host, including http/s protocol. Can
                   be passed as GENCOVE_HOST environment variable. Defaults to
                   https://api.gencove.com
  --email TEXT     Gencove user email to be used in login. Can be passed as
                   GENCOVE_EMAIL environment variable.
  --password TEXT  Gencove user password to be used in login. Can be passed as
                   GENCOVE_PASSWORD environment variable. When MFA is
                   configured, an MFA token will have to be provided after the
                   command is executed.
  --api-key TEXT   Gencove api key. Can be passed as GENCOVE_API_KEY
                   environment variable. When using the API key, an MFA token
                   does not need to be provided.
  --help           Show this message and exit.

gencove basespace biosamples

BaseSpace Biosamples management commands.

Usage:

gencove basespace biosamples [OPTIONS] COMMAND [ARGS]...

Options:

  --help  Show this message and exit.

Subcommands

  • list: List all Biosamples from BaseSpace project.

gencove basespace biosamples list

List all Biosamples from BaseSpace project.

BASESPACE_PROJECT_ID: BaseSpace project ID

Examples:

List Biosamples of a BaseSpace project:

    gencove basespace biosamples list 12345678

List Biosamples of a BaseSpace projects:

    gencove basespace biosamples list 12345678,87654321

Usage:

gencove basespace biosamples list [OPTIONS] BASESPACE_PROJECT_ID

Options:

  --host TEXT      Optional Gencove API host, including http/s protocol. Can
                   be passed as GENCOVE_HOST environment variable. Defaults to
                   https://api.gencove.com
  --email TEXT     Gencove user email to be used in login. Can be passed as
                   GENCOVE_EMAIL environment variable.
  --password TEXT  Gencove user password to be used in login. Can be passed as
                   GENCOVE_PASSWORD environment variable. When MFA is
                   configured, an MFA token will have to be provided after the
                   command is executed.
  --api-key TEXT   Gencove api key. Can be passed as GENCOVE_API_KEY
                   environment variable. When using the API key, an MFA token
                   does not need to be provided.
  --help           Show this message and exit.

gencove basespace projects

BaseSpace projects management commands.

Usage:

gencove basespace projects [OPTIONS] COMMAND [ARGS]...

Options:

  --help  Show this message and exit.

Subcommands

  • import: Import all Biosamples from BaseSpace projects to a project. Optionally add
  • list: List all BaseSpace projects.

gencove basespace projects import

Import all Biosamples from BaseSpace projects to a project. Optionally add metadata to the samples.

BASESPACE_PROJECT_IDS: comma separated list of BaseSpace project ID

PROJECT_ID: Gencove project ID

Examples:

Import Biosamples to a project:

    gencove basespace projects import 12345678 06a5d04b-526a-4471-83ba-fb54e0941758

Import Biosamples from multiple BaseSpace projects to a project:

    gencove basespace projects import 12345678,87654321 06a5d04b-526a-4471-83ba-fb54e0941758

Import Biosamples to a project with metadata:

    gencove basespace projects import 12345678 06a5d04b-526a-4471-83ba-fb54e0941758 --metadata-json='{"batch": "batch1"}'

Usage:

gencove basespace projects import [OPTIONS] BASESPACE_PROJECT_IDS PROJECT_ID

Options:

  --metadata-json TEXT  Add metadata to all samples that are to be imported
                        from BaseSpace to a project.
  --host TEXT           Optional Gencove API host, including http/s protocol.
                        Can be passed as GENCOVE_HOST environment variable.
                        Defaults to https://api.gencove.com
  --email TEXT          Gencove user email to be used in login. Can be passed
                        as GENCOVE_EMAIL environment variable.
  --password TEXT       Gencove user password to be used in login. Can be
                        passed as GENCOVE_PASSWORD environment variable. When
                        MFA is configured, an MFA token will have to be
                        provided after the command is executed.
  --api-key TEXT        Gencove api key. Can be passed as GENCOVE_API_KEY
                        environment variable. When using the API key, an MFA
                        token does not need to be provided.
  --help                Show this message and exit.

gencove basespace projects list

List all BaseSpace projects.

Examples:

Import Biosamples to a project:

    gencove basespace projects list

Usage:

gencove basespace projects list [OPTIONS]

Options:

  --host TEXT      Optional Gencove API host, including http/s protocol. Can
                   be passed as GENCOVE_HOST environment variable. Defaults to
                   https://api.gencove.com
  --email TEXT     Gencove user email to be used in login. Can be passed as
                   GENCOVE_EMAIL environment variable.
  --password TEXT  Gencove user password to be used in login. Can be passed as
                   GENCOVE_PASSWORD environment variable. When MFA is
                   configured, an MFA token will have to be provided after the
                   command is executed.
  --api-key TEXT   Gencove api key. Can be passed as GENCOVE_API_KEY
                   environment variable. When using the API key, an MFA token
                   does not need to be provided.
  --help           Show this message and exit.

gencove download

Download deliverables of a project.

DESTINATION: path/to/save/deliverables/to

Must specify either project id or sample ids.

Examples:

Download all samples results:

    gencove download ./results --project-id d9eaa54b-aaac-4b85-92b0-0b564be6d7db

Download some samples:

    gencove download ./results --sample-ids 59f5c1fd-cce0-4c4c-90e2-0b6c6c525d71,7edee497-12b5-4a1d-951f-34dc8dce1c1d

Download specific deliverables:

    gencove download ./results --project-id d9eaa54b-aaac-4b85-92b0-0b564be6d7db --file-types alignment-bam,impute-vcf,fastq-r1,fastq-r2

Skip download entirely and print out the deliverables as a JSON:

    gencove download - --project-id d9eaa54b-aaac-4b85-92b0-0b564be6d7db --download-urls

Usage:

gencove download [OPTIONS] DESTINATION

Options:

  --project-id TEXT               Gencove project ID
  --sample-ids TEXT               A comma separated list of sample ids for
                                  which to download the deliverables. If not
                                  specified, download deliverables for all
                                  samples.
  --file-types TEXT               A comma separated list of deliverable file
                                  types to download. If not specified, all
                                  file types will be downloaded.
  --skip-existing / --no-skip-existing
                                  Skip downloading files that already exist in
                                  DESTINATION
  --download-urls                 Output a list of file urls available for
                                  download in a JSON format.
  --download-template TEXT        Change downloads structure. Defaults to:
                                  {client_id}/{gencove_id}/{default_filename}.
                                  Available tokens:  {client_id} {gencove_id}
                                  {file_type} {file_extension}
                                  {default_filename}
  --host TEXT                     Optional Gencove API host, including http/s
                                  protocol. Can be passed as GENCOVE_HOST
                                  environment variable. Defaults to
                                  https://api.gencove.com
  --email TEXT                    Gencove user email to be used in login. Can
                                  be passed as GENCOVE_EMAIL environment
                                  variable.
  --password TEXT                 Gencove user password to be used in login.
                                  Can be passed as GENCOVE_PASSWORD
                                  environment variable. When MFA is
                                  configured, an MFA token will have to be
                                  provided after the command is executed.
  --api-key TEXT                  Gencove api key. Can be passed as
                                  GENCOVE_API_KEY environment variable. When
                                  using the API key, an MFA token does not
                                  need to be provided.
  --no-progress                   If specified, no progress bar is shown.
  --checksums                     If specified, an additional checksum file
                                  will be downloaded for each deliverable.
  --help                          Show this message and exit.

gencove explorer

Gencove Explorer commands.

Usage:

gencove explorer [OPTIONS] COMMAND [ARGS]...

Options:

  --help  Show this message and exit.

Subcommands

  • data: Explorer instances management commands.
  • instances: Explorer instances management commands.

gencove explorer data

Explorer instances management commands.

Usage:

gencove explorer data [OPTIONS] COMMAND [ARGS]...

Options:

  --help  Show this message and exit.

Subcommands

  • cp: Copy data to/from Explorer object storage
  • ls: List data in Explorer object storage
  • rm: Remove data from Explorer object storage
  • sync: Sync directories to/from Explorer object storage

gencove explorer data cp

Copy data to/from Explorer object storage

Usage:

gencove explorer data cp [OPTIONS] SOURCE DESTINATION

Options:

  --host TEXT      Optional Gencove API host, including http/s protocol. Can
                   be passed as GENCOVE_HOST environment variable. Defaults to
                   https://api.gencove.com
  --email TEXT     Gencove user email to be used in login. Can be passed as
                   GENCOVE_EMAIL environment variable.
  --password TEXT  Gencove user password to be used in login. Can be passed as
                   GENCOVE_PASSWORD environment variable. When MFA is
                   configured, an MFA token will have to be provided after the
                   command is executed.
  --api-key TEXT   Gencove api key. Can be passed as GENCOVE_API_KEY
                   environment variable. When using the API key, an MFA token
                   does not need to be provided.
  --help           Show this message and exit.

gencove explorer data ls

List data in Explorer object storage

Usage:

gencove explorer data ls [OPTIONS] [PATH]

Options:

  --host TEXT      Optional Gencove API host, including http/s protocol. Can
                   be passed as GENCOVE_HOST environment variable. Defaults to
                   https://api.gencove.com
  --email TEXT     Gencove user email to be used in login. Can be passed as
                   GENCOVE_EMAIL environment variable.
  --password TEXT  Gencove user password to be used in login. Can be passed as
                   GENCOVE_PASSWORD environment variable. When MFA is
                   configured, an MFA token will have to be provided after the
                   command is executed.
  --api-key TEXT   Gencove api key. Can be passed as GENCOVE_API_KEY
                   environment variable. When using the API key, an MFA token
                   does not need to be provided.
  --help           Show this message and exit.

gencove explorer data rm

Remove data from Explorer object storage

Usage:

gencove explorer data rm [OPTIONS] PATH

Options:

  --host TEXT      Optional Gencove API host, including http/s protocol. Can
                   be passed as GENCOVE_HOST environment variable. Defaults to
                   https://api.gencove.com
  --email TEXT     Gencove user email to be used in login. Can be passed as
                   GENCOVE_EMAIL environment variable.
  --password TEXT  Gencove user password to be used in login. Can be passed as
                   GENCOVE_PASSWORD environment variable. When MFA is
                   configured, an MFA token will have to be provided after the
                   command is executed.
  --api-key TEXT   Gencove api key. Can be passed as GENCOVE_API_KEY
                   environment variable. When using the API key, an MFA token
                   does not need to be provided.
  --help           Show this message and exit.

gencove explorer data sync

Sync directories to/from Explorer object storage

Usage:

gencove explorer data sync [OPTIONS] SOURCE DESTINATION

Options:

  --host TEXT      Optional Gencove API host, including http/s protocol. Can
                   be passed as GENCOVE_HOST environment variable. Defaults to
                   https://api.gencove.com
  --email TEXT     Gencove user email to be used in login. Can be passed as
                   GENCOVE_EMAIL environment variable.
  --password TEXT  Gencove user password to be used in login. Can be passed as
                   GENCOVE_PASSWORD environment variable. When MFA is
                   configured, an MFA token will have to be provided after the
                   command is executed.
  --api-key TEXT   Gencove api key. Can be passed as GENCOVE_API_KEY
                   environment variable. When using the API key, an MFA token
                   does not need to be provided.
  --help           Show this message and exit.

gencove explorer instances

Explorer instances management commands.

Usage:

gencove explorer instances [OPTIONS] COMMAND [ARGS]...

Options:

  --help  Show this message and exit.

Subcommands

  • inactivity-stop: Stop instances after hours of inactivity.
  • list: List instances.
  • shell: Start explorer shell session.
  • start: Start instances.
  • stop: Stop instances.

gencove explorer instances inactivity-stop

Stop instances after hours of inactivity. An instance can be configured to be stopped after some time of inactivity. Aditionally, this configuration can also be set at an Organization-level. By default the instance configuration has precedence over the org-level config, but this can be changed with the --override flag.

Usage:

gencove explorer instances inactivity-stop [OPTIONS]

Options:

  --hours TEXT        Amount of hours of inactivity to wait before stopping
                      instances. If hours == 0 then the instances are not
                      stopped. If hours == None then the org-level config is
                      applied.
  --organization      Sets the config for the entire Organization.
  --override BOOLEAN  Organization config overrides the instances configs.
  --host TEXT         Optional Gencove API host, including http/s protocol.
                      Can be passed as GENCOVE_HOST environment variable.
                      Defaults to https://api.gencove.com
  --email TEXT        Gencove user email to be used in login. Can be passed as
                      GENCOVE_EMAIL environment variable.
  --password TEXT     Gencove user password to be used in login. Can be passed
                      as GENCOVE_PASSWORD environment variable. When MFA is
                      configured, an MFA token will have to be provided after
                      the command is executed.
  --api-key TEXT      Gencove api key. Can be passed as GENCOVE_API_KEY
                      environment variable. When using the API key, an MFA
                      token does not need to be provided.
  --help              Show this message and exit.

gencove explorer instances list

List instances.

Usage:

gencove explorer instances list [OPTIONS]

Options:

  --host TEXT      Optional Gencove API host, including http/s protocol. Can
                   be passed as GENCOVE_HOST environment variable. Defaults to
                   https://api.gencove.com
  --email TEXT     Gencove user email to be used in login. Can be passed as
                   GENCOVE_EMAIL environment variable.
  --password TEXT  Gencove user password to be used in login. Can be passed as
                   GENCOVE_PASSWORD environment variable. When MFA is
                   configured, an MFA token will have to be provided after the
                   command is executed.
  --api-key TEXT   Gencove api key. Can be passed as GENCOVE_API_KEY
                   environment variable. When using the API key, an MFA token
                   does not need to be provided.
  --help           Show this message and exit.

gencove explorer instances shell

Start explorer shell session.

Usage:

gencove explorer instances shell [OPTIONS]

Options:

  --host TEXT      Optional Gencove API host, including http/s protocol. Can
                   be passed as GENCOVE_HOST environment variable. Defaults to
                   https://api.gencove.com
  --email TEXT     Gencove user email to be used in login. Can be passed as
                   GENCOVE_EMAIL environment variable.
  --password TEXT  Gencove user password to be used in login. Can be passed as
                   GENCOVE_PASSWORD environment variable. When MFA is
                   configured, an MFA token will have to be provided after the
                   command is executed.
  --api-key TEXT   Gencove api key. Can be passed as GENCOVE_API_KEY
                   environment variable. When using the API key, an MFA token
                   does not need to be provided.
  --help           Show this message and exit.

gencove explorer instances start

Start instances.

Usage:

gencove explorer instances start [OPTIONS]

Options:

  --host TEXT      Optional Gencove API host, including http/s protocol. Can
                   be passed as GENCOVE_HOST environment variable. Defaults to
                   https://api.gencove.com
  --email TEXT     Gencove user email to be used in login. Can be passed as
                   GENCOVE_EMAIL environment variable.
  --password TEXT  Gencove user password to be used in login. Can be passed as
                   GENCOVE_PASSWORD environment variable. When MFA is
                   configured, an MFA token will have to be provided after the
                   command is executed.
  --api-key TEXT   Gencove api key. Can be passed as GENCOVE_API_KEY
                   environment variable. When using the API key, an MFA token
                   does not need to be provided.
  --help           Show this message and exit.

gencove explorer instances stop

Stop instances.

Usage:

gencove explorer instances stop [OPTIONS]

Options:

  --host TEXT      Optional Gencove API host, including http/s protocol. Can
                   be passed as GENCOVE_HOST environment variable. Defaults to
                   https://api.gencove.com
  --email TEXT     Gencove user email to be used in login. Can be passed as
                   GENCOVE_EMAIL environment variable.
  --password TEXT  Gencove user password to be used in login. Can be passed as
                   GENCOVE_PASSWORD environment variable. When MFA is
                   configured, an MFA token will have to be provided after the
                   command is executed.
  --api-key TEXT   Gencove api key. Can be passed as GENCOVE_API_KEY
                   environment variable. When using the API key, an MFA token
                   does not need to be provided.
  --help           Show this message and exit.

gencove file-types

List file types in Gencove's system.

Usage:

gencove file-types [OPTIONS]

Options:

  --project-id TEXT               Gencove project ID
  --object [sample|reference_genome]
                                  File types of a specific object
  --host TEXT                     Optional Gencove API host, including http/s
                                  protocol. Can be passed as GENCOVE_HOST
                                  environment variable. Defaults to
                                  https://api.gencove.com
  --email TEXT                    Gencove user email to be used in login. Can
                                  be passed as GENCOVE_EMAIL environment
                                  variable.
  --password TEXT                 Gencove user password to be used in login.
                                  Can be passed as GENCOVE_PASSWORD
                                  environment variable. When MFA is
                                  configured, an MFA token will have to be
                                  provided after the command is executed.
  --api-key TEXT                  Gencove api key. Can be passed as
                                  GENCOVE_API_KEY environment variable. When
                                  using the API key, an MFA token does not
                                  need to be provided.
  --help                          Show this message and exit.

gencove projects

Project managements commands.

Usage:

gencove projects [OPTIONS] COMMAND [ARGS]...

Options:

  --help  Show this message and exit.

Subcommands

gencove projects create

Create a project.

PROJECT_NAME: name of the Gencove project

PIPELINE_CAPABILITY_ID: id of the pipeline capability to be used for the project

Usage:

gencove projects create [OPTIONS] PROJECT_NAME PIPELINE_CAPABILITY_ID

Options:

  --host TEXT      Optional Gencove API host, including http/s protocol. Can
                   be passed as GENCOVE_HOST environment variable. Defaults to
                   https://api.gencove.com
  --email TEXT     Gencove user email to be used in login. Can be passed as
                   GENCOVE_EMAIL environment variable.
  --password TEXT  Gencove user password to be used in login. Can be passed as
                   GENCOVE_PASSWORD environment variable. When MFA is
                   configured, an MFA token will have to be provided after the
                   command is executed.
  --api-key TEXT   Gencove api key. Can be passed as GENCOVE_API_KEY
                   environment variable. When using the API key, an MFA token
                   does not need to be provided.
  --help           Show this message and exit.

gencove projects create-batch

Create a batch in a project.

PROJECT_ID: Gencove project ID

Usage:

gencove projects create-batch [OPTIONS] PROJECT_ID

Options:

  --batch-type TEXT  One of available project's batch types. Use `gencove
                     projects list-batch-types` command to find out which
                     batch types are available.
  --batch-name TEXT  User defined batch name.
  --sample-ids TEXT  A comma separated list of sample ids for which to create
                     a batch; if not specified use all samples in project
  --host TEXT        Optional Gencove API host, including http/s protocol. Can
                     be passed as GENCOVE_HOST environment variable. Defaults
                     to https://api.gencove.com
  --email TEXT       Gencove user email to be used in login. Can be passed as
                     GENCOVE_EMAIL environment variable.
  --password TEXT    Gencove user password to be used in login. Can be passed
                     as GENCOVE_PASSWORD environment variable. When MFA is
                     configured, an MFA token will have to be provided after
                     the command is executed.
  --api-key TEXT     Gencove api key. Can be passed as GENCOVE_API_KEY
                     environment variable. When using the API key, an MFA
                     token does not need to be provided.
  --help             Show this message and exit.

gencove projects create-merged-vcf

Merge VCF files in a project.

PROJECT_ID: Gencove project ID

Usage:

gencove projects create-merged-vcf [OPTIONS] PROJECT_ID

Options:

  --host TEXT      Optional Gencove API host, including http/s protocol. Can
                   be passed as GENCOVE_HOST environment variable. Defaults to
                   https://api.gencove.com
  --email TEXT     Gencove user email to be used in login. Can be passed as
                   GENCOVE_EMAIL environment variable.
  --password TEXT  Gencove user password to be used in login. Can be passed as
                   GENCOVE_PASSWORD environment variable. When MFA is
                   configured, an MFA token will have to be provided after the
                   command is executed.
  --api-key TEXT   Gencove api key. Can be passed as GENCOVE_API_KEY
                   environment variable. When using the API key, an MFA token
                   does not need to be provided.
  --help           Show this message and exit.

gencove projects create-sample-manifest

Create a sample manifest in a project by uploading a CSV file.

PROJECT_ID: Gencove project ID

SAMPLE_MANIFEST: .csv file files that contains a table of information about a sequencing run

Usage:

gencove projects create-sample-manifest [OPTIONS] PROJECT_ID SAMPLE_MANIFEST

Options:

  --host TEXT      Optional Gencove API host, including http/s protocol. Can
                   be passed as GENCOVE_HOST environment variable. Defaults to
                   https://api.gencove.com
  --email TEXT     Gencove user email to be used in login. Can be passed as
                   GENCOVE_EMAIL environment variable.
  --password TEXT  Gencove user password to be used in login. Can be passed as
                   GENCOVE_PASSWORD environment variable. When MFA is
                   configured, an MFA token will have to be provided after the
                   command is executed.
  --api-key TEXT   Gencove api key. Can be passed as GENCOVE_API_KEY
                   environment variable. When using the API key, an MFA token
                   does not need to be provided.
  --help           Show this message and exit.

gencove projects delete

Delete projects.

PROJECT_IDS: comma-separted list of projects to be deleted.

Usage:

gencove projects delete [OPTIONS] PROJECT_IDS

Options:

  --host TEXT      Optional Gencove API host, including http/s protocol. Can
                   be passed as GENCOVE_HOST environment variable. Defaults to
                   https://api.gencove.com
  --email TEXT     Gencove user email to be used in login. Can be passed as
                   GENCOVE_EMAIL environment variable.
  --password TEXT  Gencove user password to be used in login. Can be passed as
                   GENCOVE_PASSWORD environment variable. When MFA is
                   configured, an MFA token will have to be provided after the
                   command is executed.
  --api-key TEXT   Gencove api key. Can be passed as GENCOVE_API_KEY
                   environment variable. When using the API key, an MFA token
                   does not need to be provided.
  --help           Show this message and exit.

gencove projects delete-samples

Delete samples in a project.

PROJECT_ID: Gencove project ID

Usage:

gencove projects delete-samples [OPTIONS] PROJECT_ID

Options:

  --sample-ids TEXT  A comma separated list of sample ids which will be
                     deleted.
  --host TEXT        Optional Gencove API host, including http/s protocol. Can
                     be passed as GENCOVE_HOST environment variable. Defaults
                     to https://api.gencove.com
  --email TEXT       Gencove user email to be used in login. Can be passed as
                     GENCOVE_EMAIL environment variable.
  --password TEXT    Gencove user password to be used in login. Can be passed
                     as GENCOVE_PASSWORD environment variable. When MFA is
                     configured, an MFA token will have to be provided after
                     the command is executed.
  --api-key TEXT     Gencove api key. Can be passed as GENCOVE_API_KEY
                     environment variable. When using the API key, an MFA
                     token does not need to be provided.
  --help             Show this message and exit.

gencove projects get-batch

Get batch that is available for a project.

BATCH_ID: project's batch ID

Usage:

gencove projects get-batch [OPTIONS] BATCH_ID

Options:

  --output-filename PATH  Output filename for batch deliverable.
  --host TEXT             Optional Gencove API host, including http/s
                          protocol. Can be passed as GENCOVE_HOST environment
                          variable. Defaults to https://api.gencove.com
  --email TEXT            Gencove user email to be used in login. Can be
                          passed as GENCOVE_EMAIL environment variable.
  --password TEXT         Gencove user password to be used in login. Can be
                          passed as GENCOVE_PASSWORD environment variable.
                          When MFA is configured, an MFA token will have to be
                          provided after the command is executed.
  --api-key TEXT          Gencove api key. Can be passed as GENCOVE_API_KEY
                          environment variable. When using the API key, an MFA
                          token does not need to be provided.
  --no-progress           If specified, no progress bar is shown.
  --help                  Show this message and exit.

gencove projects get-merged-vcf

Download merged VCF file in a project.

PROJECT_ID: Gencove project ID

Usage:

gencove projects get-merged-vcf [OPTIONS] PROJECT_ID

Options:

  --output-filename PATH  Output filename for merged VCF file.
  --host TEXT             Optional Gencove API host, including http/s
                          protocol. Can be passed as GENCOVE_HOST environment
                          variable. Defaults to https://api.gencove.com
  --email TEXT            Gencove user email to be used in login. Can be
                          passed as GENCOVE_EMAIL environment variable.
  --password TEXT         Gencove user password to be used in login. Can be
                          passed as GENCOVE_PASSWORD environment variable.
                          When MFA is configured, an MFA token will have to be
                          provided after the command is executed.
  --api-key TEXT          Gencove api key. Can be passed as GENCOVE_API_KEY
                          environment variable. When using the API key, an MFA
                          token does not need to be provided.
  --no-progress           If specified, no progress bar is shown.
  --help                  Show this message and exit.

gencove projects get-reference-genome

Download Reference genomes of a project

PROJECT_ID: Gencove project ID DESTINATION: path/to/save/deliverables/to

Examples:

Download all reference genome files:

    gencove projects get_reference_genome d9eaa54b-aaac-4b85-92b0-0b564be6d7db
     ./genome


Download only fasta reference genome file:

    gencove projects get_reference_genome d9eaa54b-aaac-4b85-92b0-0b564be6d7db
     . --file-types genome-fasta

Usage:

gencove projects get-reference-genome [OPTIONS] PROJECT_ID DESTINATION

Options:

  --file-types TEXT  A comma separated list of deliverable file types to
                     download. If not specified, all file types will be
                     downloaded.
  --host TEXT        Optional Gencove API host, including http/s protocol. Can
                     be passed as GENCOVE_HOST environment variable. Defaults
                     to https://api.gencove.com
  --email TEXT       Gencove user email to be used in login. Can be passed as
                     GENCOVE_EMAIL environment variable.
  --password TEXT    Gencove user password to be used in login. Can be passed
                     as GENCOVE_PASSWORD environment variable. When MFA is
                     configured, an MFA token will have to be provided after
                     the command is executed.
  --api-key TEXT     Gencove api key. Can be passed as GENCOVE_API_KEY
                     environment variable. When using the API key, an MFA
                     token does not need to be provided.
  --no-progress      If specified, no progress bar is shown.
  --help             Show this message and exit.

gencove projects get-sample-manifests

Download all sample manifests in a project to a destination directory.

PROJECT_ID: Gencove project ID

DESTINATION: path/to/save/sample/manifests/to

Usage:

gencove projects get-sample-manifests [OPTIONS] PROJECT_ID DESTINATION

Options:

  --host TEXT      Optional Gencove API host, including http/s protocol. Can
                   be passed as GENCOVE_HOST environment variable. Defaults to
                   https://api.gencove.com
  --email TEXT     Gencove user email to be used in login. Can be passed as
                   GENCOVE_EMAIL environment variable.
  --password TEXT  Gencove user password to be used in login. Can be passed as
                   GENCOVE_PASSWORD environment variable. When MFA is
                   configured, an MFA token will have to be provided after the
                   command is executed.
  --api-key TEXT   Gencove api key. Can be passed as GENCOVE_API_KEY
                   environment variable. When using the API key, an MFA token
                   does not need to be provided.
  --help           Show this message and exit.

gencove projects import-existing-samples

Import existing samples to a project.

PROJECT_ID: Gencove project ID

Examples:

Import samples:

    gencove project import-existing-samples d9eaa54b-aaac-4b85-92b0-0b564be6d7db --sample-ids 59f5c1fd-cce0-4c4c-90e2-0b6c6c525d71,7edee497-12b5-4a1d-951f-34dc8dce1c1d

Import samples with metadata:

    gencove project import-existing-samples d9eaa54b-aaac-4b85-92b0-0b564be6d7db --sample-ids 59f5c1fd-cce0-4c4c-90e2-0b6c6c525d71,7edee497-12b5-4a1d-951f-34dc8dce1c1d --metadata-json='{"batch": "batch1"}'

Usage:

gencove projects import-existing-samples [OPTIONS] PROJECT_ID

Options:

  --sample-ids TEXT     A comma separated list of sample ids to import into
                        the provided project  [required]
  --metadata-json TEXT  Add metadata to all samples that are to be imported
                        into a project.
  --host TEXT           Optional Gencove API host, including http/s protocol.
                        Can be passed as GENCOVE_HOST environment variable.
                        Defaults to https://api.gencove.com
  --email TEXT          Gencove user email to be used in login. Can be passed
                        as GENCOVE_EMAIL environment variable.
  --password TEXT       Gencove user password to be used in login. Can be
                        passed as GENCOVE_PASSWORD environment variable. When
                        MFA is configured, an MFA token will have to be
                        provided after the command is executed.
  --api-key TEXT        Gencove api key. Can be passed as GENCOVE_API_KEY
                        environment variable. When using the API key, an MFA
                        token does not need to be provided.
  --help                Show this message and exit.

gencove projects list

List your projects.

Usage:

gencove projects list [OPTIONS]

Options:

  --include-capability / --no-include-capability
                                  Include capability id and key
  --host TEXT                     Optional Gencove API host, including http/s
                                  protocol. Can be passed as GENCOVE_HOST
                                  environment variable. Defaults to
                                  https://api.gencove.com
  --email TEXT                    Gencove user email to be used in login. Can
                                  be passed as GENCOVE_EMAIL environment
                                  variable.
  --password TEXT                 Gencove user password to be used in login.
                                  Can be passed as GENCOVE_PASSWORD
                                  environment variable. When MFA is
                                  configured, an MFA token will have to be
                                  provided after the command is executed.
  --api-key TEXT                  Gencove api key. Can be passed as
                                  GENCOVE_API_KEY environment variable. When
                                  using the API key, an MFA token does not
                                  need to be provided.
  --help                          Show this message and exit.

gencove projects list-batch-types

List batch types that are available for a project.

PROJECT_ID: Gencove project ID

Usage:

gencove projects list-batch-types [OPTIONS] PROJECT_ID

Options:

  --host TEXT      Optional Gencove API host, including http/s protocol. Can
                   be passed as GENCOVE_HOST environment variable. Defaults to
                   https://api.gencove.com
  --email TEXT     Gencove user email to be used in login. Can be passed as
                   GENCOVE_EMAIL environment variable.
  --password TEXT  Gencove user password to be used in login. Can be passed as
                   GENCOVE_PASSWORD environment variable. When MFA is
                   configured, an MFA token will have to be provided after the
                   command is executed.
  --api-key TEXT   Gencove api key. Can be passed as GENCOVE_API_KEY
                   environment variable. When using the API key, an MFA token
                   does not need to be provided.
  --help           Show this message and exit.

gencove projects list-batches

List batches that are available for a project.

PROJECT_ID: Gencove project ID

Usage:

gencove projects list-batches [OPTIONS] PROJECT_ID

Options:

  --host TEXT      Optional Gencove API host, including http/s protocol. Can
                   be passed as GENCOVE_HOST environment variable. Defaults to
                   https://api.gencove.com
  --email TEXT     Gencove user email to be used in login. Can be passed as
                   GENCOVE_EMAIL environment variable.
  --password TEXT  Gencove user password to be used in login. Can be passed as
                   GENCOVE_PASSWORD environment variable. When MFA is
                   configured, an MFA token will have to be provided after the
                   command is executed.
  --api-key TEXT   Gencove api key. Can be passed as GENCOVE_API_KEY
                   environment variable. When using the API key, an MFA token
                   does not need to be provided.
  --help           Show this message and exit.

gencove projects list-pipeline-capabilities

List pipeline capabilities that are available for a pipeline.

PIPELINE_ID: pipeline ID

Usage:

gencove projects list-pipeline-capabilities [OPTIONS] PIPELINE_ID

Options:

  --host TEXT      Optional Gencove API host, including http/s protocol. Can
                   be passed as GENCOVE_HOST environment variable. Defaults to
                   https://api.gencove.com
  --email TEXT     Gencove user email to be used in login. Can be passed as
                   GENCOVE_EMAIL environment variable.
  --password TEXT  Gencove user password to be used in login. Can be passed as
                   GENCOVE_PASSWORD environment variable. When MFA is
                   configured, an MFA token will have to be provided after the
                   command is executed.
  --api-key TEXT   Gencove api key. Can be passed as GENCOVE_API_KEY
                   environment variable. When using the API key, an MFA token
                   does not need to be provided.
  --help           Show this message and exit.

gencove projects list-pipelines

List pipelines that are available when creating a project.

Usage:

gencove projects list-pipelines [OPTIONS]

Options:

  --host TEXT      Optional Gencove API host, including http/s protocol. Can
                   be passed as GENCOVE_HOST environment variable. Defaults to
                   https://api.gencove.com
  --email TEXT     Gencove user email to be used in login. Can be passed as
                   GENCOVE_EMAIL environment variable.
  --password TEXT  Gencove user password to be used in login. Can be passed as
                   GENCOVE_PASSWORD environment variable. When MFA is
                   configured, an MFA token will have to be provided after the
                   command is executed.
  --api-key TEXT   Gencove api key. Can be passed as GENCOVE_API_KEY
                   environment variable. When using the API key, an MFA token
                   does not need to be provided.
  --help           Show this message and exit.

gencove projects list-samples

List samples in a project.

PROJECT_ID: Gencove project ID

Usage:

gencove projects list-samples [OPTIONS] PROJECT_ID

Options:

  --search TEXT                   Gencove sample ID, client ID or metadata
                                  substring
  --status [completed|succeeded|failed|running|all]
                                  Get samples with specific status
  --archive-status [available|archived|restore_requested|all|unknown]
                                  Get samples with specific archive status
  --include-run / --no-include-run
                                  Include run id
  --host TEXT                     Optional Gencove API host, including http/s
                                  protocol. Can be passed as GENCOVE_HOST
                                  environment variable. Defaults to
                                  https://api.gencove.com
  --email TEXT                    Gencove user email to be used in login. Can
                                  be passed as GENCOVE_EMAIL environment
                                  variable.
  --password TEXT                 Gencove user password to be used in login.
                                  Can be passed as GENCOVE_PASSWORD
                                  environment variable. When MFA is
                                  configured, an MFA token will have to be
                                  provided after the command is executed.
  --api-key TEXT                  Gencove api key. Can be passed as
                                  GENCOVE_API_KEY environment variable. When
                                  using the API key, an MFA token does not
                                  need to be provided.
  --help                          Show this message and exit.

gencove projects restore-samples

Restore samples in a project.

PROJECT_ID: Gencove project ID

Usage:

gencove projects restore-samples [OPTIONS] PROJECT_ID

Options:

  --sample-ids TEXT  A comma separated list of sample ids which will be
                     restored. If omitted, restores all archived samples in
                     project.
  --host TEXT        Optional Gencove API host, including http/s protocol. Can
                     be passed as GENCOVE_HOST environment variable. Defaults
                     to https://api.gencove.com
  --email TEXT       Gencove user email to be used in login. Can be passed as
                     GENCOVE_EMAIL environment variable.
  --password TEXT    Gencove user password to be used in login. Can be passed
                     as GENCOVE_PASSWORD environment variable. When MFA is
                     configured, an MFA token will have to be provided after
                     the command is executed.
  --api-key TEXT     Gencove api key. Can be passed as GENCOVE_API_KEY
                     environment variable. When using the API key, an MFA
                     token does not need to be provided.
  --help             Show this message and exit.

gencove projects run-prefix

Assign all uploads from Gencove prefix to a project. Optionally add metadata to the samples. Uploads can also be filtered through status.

PROJECT_ID: Gencove project ID

RUN_PREFIX: Gencove prefix where samples are located formated as gncv://path

Examples:

Assign uploads to a project:

    gencove projects run-prefix 06a5d04b-526a-4471-83ba-fb54e0941758 gncv://my-project/path

Assign uploads to a project with metadata:

    gencove projects run-prefix 06a5d04b-526a-4471-83ba-fb54e0941758 gncv://my-project/path --metadata-json='{"batch": "batch1"}'

Assign uploads filtered by status to a project:

    gencove projects run-prefix 06a5d04b-526a-4471-83ba-fb54e0941758 gncv://my-project/path --status assigned

Usage:

gencove projects run-prefix [OPTIONS] PROJECT_ID PREFIX

Options:

  --metadata-json TEXT            Add metadata to all uploads that are to be
                                  assigned to a project.
  --status [all|unassigned|assigned]
                                  Filter uploads by status of assignment
  --host TEXT                     Optional Gencove API host, including http/s
                                  protocol. Can be passed as GENCOVE_HOST
                                  environment variable. Defaults to
                                  https://api.gencove.com
  --email TEXT                    Gencove user email to be used in login. Can
                                  be passed as GENCOVE_EMAIL environment
                                  variable.
  --password TEXT                 Gencove user password to be used in login.
                                  Can be passed as GENCOVE_PASSWORD
                                  environment variable. When MFA is
                                  configured, an MFA token will have to be
                                  provided after the command is executed.
  --api-key TEXT                  Gencove api key. Can be passed as
                                  GENCOVE_API_KEY environment variable. When
                                  using the API key, an MFA token does not
                                  need to be provided.
  --help                          Show this message and exit.

gencove projects status-merged-vcf

Get status of merge VCF files job in a project.

PROJECT_ID: Gencove project ID

Usage:

gencove projects status-merged-vcf [OPTIONS] PROJECT_ID

Options:

  --host TEXT      Optional Gencove API host, including http/s protocol. Can
                   be passed as GENCOVE_HOST environment variable. Defaults to
                   https://api.gencove.com
  --email TEXT     Gencove user email to be used in login. Can be passed as
                   GENCOVE_EMAIL environment variable.
  --password TEXT  Gencove user password to be used in login. Can be passed as
                   GENCOVE_PASSWORD environment variable. When MFA is
                   configured, an MFA token will have to be provided after the
                   command is executed.
  --api-key TEXT   Gencove api key. Can be passed as GENCOVE_API_KEY
                   environment variable. When using the API key, an MFA token
                   does not need to be provided.
  --help           Show this message and exit.

gencove reports

Report management commands.

Usage:

gencove reports [OPTIONS] COMMAND [ARGS]...

Options:

  --help  Show this message and exit.

Subcommands

  • monthly-usage: Get monthly usage report for organization.
  • project-qc: Download a project QC CSV report to a specified filename.

gencove reports monthly-usage

Get monthly usage report for organization. If --to and --from parameters are not supplied, the last 12 months of usage are retrieved.

Usage:

gencove reports monthly-usage [OPTIONS]

Options:

  --from TEXT             Date to start report from in format YYYY-MM, e.g.
                          2023-01. If supplied, --to parameter must also be
                          supplied.
  --to TEXT               Date to end report at in format YYYY-MM, e.g.
                          2023-03. If supplied, --from parameter must also be
                          supplied.
  --output-filename PATH  Output filename for the output report. If not
                          supplied, will download the file to the current
                          directory.
  --host TEXT             Optional Gencove API host, including http/s
                          protocol. Can be passed as GENCOVE_HOST environment
                          variable. Defaults to https://api.gencove.com
  --email TEXT            Gencove user email to be used in login. Can be
                          passed as GENCOVE_EMAIL environment variable.
  --password TEXT         Gencove user password to be used in login. Can be
                          passed as GENCOVE_PASSWORD environment variable.
                          When MFA is configured, an MFA token will have to be
                          provided after the command is executed.
  --api-key TEXT          Gencove api key. Can be passed as GENCOVE_API_KEY
                          environment variable. When using the API key, an MFA
                          token does not need to be provided.
  --help                  Show this message and exit.

gencove reports project-qc

Download a project QC CSV report to a specified filename.

PROJECT_ID: Gencove project ID

Usage:

gencove reports project-qc [OPTIONS] PROJECT_ID

Options:

  --columns TEXT          A comma separated list of columns to include in the
                          report. By default, all columns are included.
  --output-filename PATH  Output filename for the output report. If not
                          supplied, will download the file to the current
                          directory.
  --host TEXT             Optional Gencove API host, including http/s
                          protocol. Can be passed as GENCOVE_HOST environment
                          variable. Defaults to https://api.gencove.com
  --email TEXT            Gencove user email to be used in login. Can be
                          passed as GENCOVE_EMAIL environment variable.
  --password TEXT         Gencove user password to be used in login. Can be
                          passed as GENCOVE_PASSWORD environment variable.
                          When MFA is configured, an MFA token will have to be
                          provided after the command is executed.
  --api-key TEXT          Gencove api key. Can be passed as GENCOVE_API_KEY
                          environment variable. When using the API key, an MFA
                          token does not need to be provided.
  --help                  Show this message and exit.

gencove s3

S3 imports managements commands. Setup guide: https://docs.gencove.com/main/s3-imports/

Usage:

gencove s3 [OPTIONS] COMMAND [ARGS]...

Options:

  --help  Show this message and exit.

Subcommands

  • autoimports: S3 autoimports management commands.
  • import: Import all samples from a S3 URI to a project. Optionally add

gencove s3 autoimports

S3 autoimports management commands.

Usage:

gencove s3 autoimports [OPTIONS] COMMAND [ARGS]...

Options:

  --help  Show this message and exit.

Subcommands

  • create: Sets up automatic import from S3 URI to a project in Gencove. Optionally assign metadata to the samples to be added when the automatic
  • list: Lists S3 automatic import jobs.

gencove s3 autoimports create

Sets up automatic import from S3 URI to a project in Gencove. Optionally assign metadata to the samples to be added when the automatic import job runs.

PROJECT_ID: Gencove project ID

S3_URI: s3 prefix where samples are and will be located

Examples:

Set up automatic import from S3 to a project:

    gencove s3 autoimports create 06a5d04b-526a-4471-83ba-fb54e0941758 s3://bucket/path/to/project

Set up automatic import from S3 to a project with metadata:

    gencove s3 autoimports create 06a5d04b-526a-4471-83ba-fb54e0941758 s3://bucket/path/to/project --metadata-json='{"batch": "batch1"}'

Usage:

gencove s3 autoimports create [OPTIONS] PROJECT_ID S3_URI

Options:

  --metadata-json TEXT  Add metadata to all samples that are to be imported
                        from S3 to a project.
  --host TEXT           Optional Gencove API host, including http/s protocol.
                        Can be passed as GENCOVE_HOST environment variable.
                        Defaults to https://api.gencove.com
  --email TEXT          Gencove user email to be used in login. Can be passed
                        as GENCOVE_EMAIL environment variable.
  --password TEXT       Gencove user password to be used in login. Can be
                        passed as GENCOVE_PASSWORD environment variable. When
                        MFA is configured, an MFA token will have to be
                        provided after the command is executed.
  --api-key TEXT        Gencove api key. Can be passed as GENCOVE_API_KEY
                        environment variable. When using the API key, an MFA
                        token does not need to be provided.
  --help                Show this message and exit.

gencove s3 autoimports list

Lists S3 automatic import jobs.

Examples:

List S3 automatic import jobs:

    gencove s3 autoimports list

Usage:

gencove s3 autoimports list [OPTIONS]

Options:

  --host TEXT      Optional Gencove API host, including http/s protocol. Can
                   be passed as GENCOVE_HOST environment variable. Defaults to
                   https://api.gencove.com
  --email TEXT     Gencove user email to be used in login. Can be passed as
                   GENCOVE_EMAIL environment variable.
  --password TEXT  Gencove user password to be used in login. Can be passed as
                   GENCOVE_PASSWORD environment variable. When MFA is
                   configured, an MFA token will have to be provided after the
                   command is executed.
  --api-key TEXT   Gencove api key. Can be passed as GENCOVE_API_KEY
                   environment variable. When using the API key, an MFA token
                   does not need to be provided.
  --help           Show this message and exit.

gencove s3 import

Import all samples from a S3 URI to a project. Optionally add metadata to the samples.

S3_URI: s3 prefix where samples are located

PROJECT_ID: Gencove project ID

Examples:

Import samples to a project:

    gencove s3 import s3://bucket/path/ 06a5d04b-526a-4471-83ba-fb54e0941758

Import samples to a project:

    gencove s3 import s3://bucket/path/ 06a5d04b-526a-4471-83ba-fb54e0941758 --metadata-json='{"batch": "batch1"}'

Usage:

gencove s3 import [OPTIONS] S3_URI PROJECT_ID

Options:

  --metadata-json TEXT  Add metadata to all samples that are to be imported
                        from S3 to a project.
  --host TEXT           Optional Gencove API host, including http/s protocol.
                        Can be passed as GENCOVE_HOST environment variable.
                        Defaults to https://api.gencove.com
  --email TEXT          Gencove user email to be used in login. Can be passed
                        as GENCOVE_EMAIL environment variable.
  --password TEXT       Gencove user password to be used in login. Can be
                        passed as GENCOVE_PASSWORD environment variable. When
                        MFA is configured, an MFA token will have to be
                        provided after the command is executed.
  --api-key TEXT        Gencove api key. Can be passed as GENCOVE_API_KEY
                        environment variable. When using the API key, an MFA
                        token does not need to be provided.
  --help                Show this message and exit.

gencove sample-manifests

Sample manifest management commands.

Usage:

gencove sample-manifests [OPTIONS] COMMAND [ARGS]...

Options:

  --help  Show this message and exit.

Subcommands

gencove sample-manifests get-sample-manifest

Download a sample manifest to a specified destination directory.

MANIFEST_ID: Gencove manifest ID

DESTINATION: path/to/save/manifest/to

Usage:

gencove sample-manifests get-sample-manifest [OPTIONS] MANIFEST_ID DESTINATION

Options:

  --host TEXT      Optional Gencove API host, including http/s protocol. Can
                   be passed as GENCOVE_HOST environment variable. Defaults to
                   https://api.gencove.com
  --email TEXT     Gencove user email to be used in login. Can be passed as
                   GENCOVE_EMAIL environment variable.
  --password TEXT  Gencove user password to be used in login. Can be passed as
                   GENCOVE_PASSWORD environment variable. When MFA is
                   configured, an MFA token will have to be provided after the
                   command is executed.
  --api-key TEXT   Gencove api key. Can be passed as GENCOVE_API_KEY
                   environment variable. When using the API key, an MFA token
                   does not need to be provided.
  --help           Show this message and exit.

gencove samples

Sample managements commands.

Usage:

gencove samples [OPTIONS] COMMAND [ARGS]...

Options:

  --help  Show this message and exit.

Subcommands

gencove samples download-file

Download a single sample file. Using this command, sample file can be streamed to stdout.

SAMPLE_ID: sample for which to download the results

FILE_TYPE: specific deliverable to download results for

DESTINATION: path/to/file

Examples:

Download sample:

    gencove samples download-file e6b45af7-07c5-4a6d-9f97-6e1efbf3e215 ancestry-json ancestry.json

Download and print to stdout then compress using gzip:

    gencove samples download-file e6b45af7-07c5-4a6d-9f97-6e1efbf3e215 ancestry-json - | gzip > ancestry.json.gz

Usage:

gencove samples download-file [OPTIONS] SAMPLE_ID FILE_TYPE DESTINATION

Options:

  --host TEXT      Optional Gencove API host, including http/s protocol. Can
                   be passed as GENCOVE_HOST environment variable. Defaults to
                   https://api.gencove.com
  --email TEXT     Gencove user email to be used in login. Can be passed as
                   GENCOVE_EMAIL environment variable.
  --password TEXT  Gencove user password to be used in login. Can be passed as
                   GENCOVE_PASSWORD environment variable. When MFA is
                   configured, an MFA token will have to be provided after the
                   command is executed.
  --api-key TEXT   Gencove api key. Can be passed as GENCOVE_API_KEY
                   environment variable. When using the API key, an MFA token
                   does not need to be provided.
  --no-progress    If specified, no progress bar is shown.
  --checksum       If specified, an additional checksum file will be
                   downloaded.
  --help           Show this message and exit.

gencove samples get-metadata

Get sample metadata.

SAMPLE_ID: sample for which to get the metadata

Usage:

gencove samples get-metadata [OPTIONS] SAMPLE_ID

Options:

  --output-filename PATH  Output filename for the metadata.
  --host TEXT             Optional Gencove API host, including http/s
                          protocol. Can be passed as GENCOVE_HOST environment
                          variable. Defaults to https://api.gencove.com
  --email TEXT            Gencove user email to be used in login. Can be
                          passed as GENCOVE_EMAIL environment variable.
  --password TEXT         Gencove user password to be used in login. Can be
                          passed as GENCOVE_PASSWORD environment variable.
                          When MFA is configured, an MFA token will have to be
                          provided after the command is executed.
  --api-key TEXT          Gencove api key. Can be passed as GENCOVE_API_KEY
                          environment variable. When using the API key, an MFA
                          token does not need to be provided.
  --help                  Show this message and exit.

gencove samples set-metadata

Set sample metadata.

SAMPLE_ID: sample for which to set the metadata

Usage:

gencove samples set-metadata [OPTIONS] SAMPLE_ID

Options:

  --json TEXT      JSON string of the metadata to be assigned to a sample.
                   [required]
  --host TEXT      Optional Gencove API host, including http/s protocol. Can
                   be passed as GENCOVE_HOST environment variable. Defaults to
                   https://api.gencove.com
  --email TEXT     Gencove user email to be used in login. Can be passed as
                   GENCOVE_EMAIL environment variable.
  --password TEXT  Gencove user password to be used in login. Can be passed as
                   GENCOVE_PASSWORD environment variable. When MFA is
                   configured, an MFA token will have to be provided after the
                   command is executed.
  --api-key TEXT   Gencove api key. Can be passed as GENCOVE_API_KEY
                   environment variable. When using the API key, an MFA token
                   does not need to be provided.
  --help           Show this message and exit.

gencove upload

Upload FASTQ files to Gencove's system.

SOURCE: folder that contains fastq files to be uploaded (acceptable file extensions are .fastq.gz, .fastq.bgz, .fq.gz, .fq.bgz), OR .fastq-map.csv file with the mapping of R1/R2 files to related sample by client_id

DESTINATION (optional): gncv://[folder], where the folder is the location on Gencove systems

Examples:

Upload directory contents:

    gencove upload test_dataset gncv://test

Usage:

gencove upload [OPTIONS] SOURCE [DESTINATION]

Options:

  --host TEXT            Optional Gencove API host, including http/s protocol.
                         Can be passed as GENCOVE_HOST environment variable.
                         Defaults to https://api.gencove.com
  --email TEXT           Gencove user email to be used in login. Can be passed
                         as GENCOVE_EMAIL environment variable.
  --password TEXT        Gencove user password to be used in login. Can be
                         passed as GENCOVE_PASSWORD environment variable. When
                         MFA is configured, an MFA token will have to be
                         provided after the command is executed.
  --api-key TEXT         Gencove api key. Can be passed as GENCOVE_API_KEY
                         environment variable. When using the API key, an MFA
                         token does not need to be provided.
  --run-project-id TEXT  Immediately assign all uploaded files to this project
                         and run them
  --output TEXT          A destination where to store the resulting
                         assignments. Only compatible with --run-project-id.
  --no-progress          If specified, no progress bar is shown.
  --metadata TEXT        Assign JSON metadata to all samples created from
                         uploads. Only compatible with --run-project-id.
  --help                 Show this message and exit.

gencove uploads

Uploads management commands.

Usage:

gencove uploads [OPTIONS] COMMAND [ARGS]...

Options:

  --help  Show this message and exit.

Subcommands

  • list: List user uploads.

gencove uploads list

List user uploads.

Usage:

gencove uploads list [OPTIONS]

Options:

  --search TEXT                   Filter uploads by gncv path
  --status [all|unassigned|assigned]
                                  Filter uploads by status of assignment
  --host TEXT                     Optional Gencove API host, including http/s
                                  protocol. Can be passed as GENCOVE_HOST
                                  environment variable. Defaults to
                                  https://api.gencove.com
  --email TEXT                    Gencove user email to be used in login. Can
                                  be passed as GENCOVE_EMAIL environment
                                  variable.
  --password TEXT                 Gencove user password to be used in login.
                                  Can be passed as GENCOVE_PASSWORD
                                  environment variable. When MFA is
                                  configured, an MFA token will have to be
                                  provided after the command is executed.
  --api-key TEXT                  Gencove api key. Can be passed as
                                  GENCOVE_API_KEY environment variable. When
                                  using the API key, an MFA token does not
                                  need to be provided.
  --help                          Show this message and exit.

gencove webhooks

Webhook managements commands.

Usage:

gencove webhooks [OPTIONS] COMMAND [ARGS]...

Options:

  --help  Show this message and exit.

Subcommands

  • verify: Verify webhook signature.

gencove webhooks verify

Verify webhook signature.

SECRET: key to be used as a secret for hmac algorithm.

HEADER: Gencove-Signature header content.

PAYLOAD: JSON payload (i.e., the request’s body).

Usage:

gencove webhooks verify [OPTIONS] SECRET HEADER PAYLOAD

Options:

  --help  Show this message and exit.