CLI Reference¶
Supported Python versions are 3.8 and above.
To start using Gencove CLI Tool, open an interactive shell and run:
This will output all available commands.
gencove¶
Gencove's command line interface.
Usage:
Options:
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:
Options:
Subcommands
- autoimports: BaseSpace autoimports management commands.
- biosamples: BaseSpace Biosamples management commands.
- projects: BaseSpace projects management commands.
gencove basespace autoimports¶
BaseSpace autoimports management commands.
Usage:
Options:
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:
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. Only used if
--email is provided.
--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:
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. Only used if --email is provided.
--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:
Options:
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:
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. Only used if --email is provided.
--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:
Options:
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:
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. Only used if
--email is provided.
--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:
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. Only used if --email is provided.
--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:
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. Only
used if --email is provided.
--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:
Options:
Subcommands
gencove explorer data¶
Explorer data management commands.
Usage:
Options:
Subcommands
- archive: Archive data in Explorer object storage
- cp: Copy data to/from Explorer object storage
- ls: List data in Explorer object storage
- presign: Generate a presigned URL for an object in Explorer object storage
- restore: Restore archived data in Explorer object storage
- rm: Remove data from Explorer object storage
- sync: Sync directories to/from Explorer object storage
gencove explorer data archive¶
Archive data in Explorer object storage
Usage:
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. Only used if --email is provided.
--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 cp¶
Copy data to/from Explorer object storage
Usage:
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. Only used if --email is provided.
--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:
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. Only used if --email is provided.
--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 presign¶
Generate a presigned URL for an object in Explorer object storage
Usage:
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. Only used if --email is provided.
--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 restore¶
Restore archived data in Explorer object storage
Usage:
Options:
--days INTEGER Days that the restored data will be available for.
--tier TEXT When restoring an archived object, you can specify one of
the following data access tier options: Expedited,
Standard, Bulk.
--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. Only used if --email is provided.
--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:
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. Only used if --email is provided.
--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:
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. Only used if --email is provided.
--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:
Options:
Subcommands
- inactivity-stop: Stop instances after hours of inactivity.
- list: List instances.
- shell: Start explorer shell session.
- start: Start instances.
- stop: Stop instances.
- url: Generate shareable URL for Explorer instance.
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:
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. Only used if --email is
provided.
--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:
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. Only used if --email is provided.
--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:
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. Only used if --email is provided.
--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:
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. Only used if --email is provided.
--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:
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. Only used if --email is provided.
--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 url¶
Generate shareable URL for Explorer instance.
Usage:
Options:
--expiration-seconds INTEGER Number of seconds before the URL expires.
Maximum is 24h (86400s). [default: 86400]
--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. Only used if --email is provided.
--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:
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. Only
used if --email is provided.
--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:
Options:
Subcommands
- create: Create a project.
- create-batch: Create a batch in a project.
- create-merged-vcf: Merge VCF files in a project.
- create-sample-manifest: Create a sample manifest in a project by uploading a CSV file.
- delete: Delete projects.
- delete-samples: Delete samples in a project.
- get-batch: Get batch that is available for a project.
- get-merged-vcf: Download merged VCF file in a project.
- get-reference-genome: Download Reference genomes of a project
- get-sample-manifests: Download all sample manifests in a project to a destination directory.
- hide: Hide projects.
- hide-samples: Hide samples in a project.
- import-existing-samples: Import existing samples to a project.
- list: List your projects.
- list-batch-types: List batch types that are available for a project.
- list-batches: List batches that are available for a project.
- list-pipeline-capabilities: List pipeline capabilities that are available for a pipeline.
- list-pipelines: List pipelines that are available when creating a project.
- list-samples: List samples in a project.
- restore-samples: Restore samples in a project.
- run-prefix: Assign all uploads from Gencove prefix to a project. Optionally add
- status-merged-vcf: Get status of merge VCF files job in a project.
- unhide: Unhide projects.
- unhide-samples: Unhide samples in a project.
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:
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. Only used if --email is provided.
--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:
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. Only used if --email is
provided.
--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:
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. Only used if --email is provided.
--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:
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. Only used if --email is provided.
--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:
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. Only used if --email is provided.
--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:
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. Only used if --email is
provided.
--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:
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. Only used if
--email is provided.
--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:
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. Only used if
--email is provided.
--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:
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. Only used if --email is
provided.
--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:
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. Only used if --email is provided.
--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 hide¶
Hide projects.
PROJECT_IDS: comma-separted list of projects to be hidden.
Usage:
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. Only used if --email is provided.
--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 hide-samples¶
Hide samples in a project.
PROJECT_ID: Gencove project ID
Usage:
Options:
--sample-ids TEXT A comma separated list of sample ids which will be
hidden.
--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. Only used if --email is
provided.
--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 from project:
gencove projects import-existing-samples d9eaa54b-aaac-4b85-92b0-0b564be6d7db --source-project-id d8eb0bb5-29ee-44ed-b681-0fc05a557183
Import samples:
gencove projects 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 projects 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:
Options:
--source-project-id, --project-id TEXT
Import all available samples, in succeeded
or failed_qc state that have files, from
source project. Either --source-project-id
or --source-sample-ids option must be
provided, but not both.
--source-sample-ids, --sample-ids TEXT
A comma separated list of source sample ids
to import into the provided project. Either
--source-project-id or --source-sample-ids
option must be provided, but not both.
--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. Only
used if --email is provided.
--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:
Options:
--include-capability / --no-include-capability
Include capability id and key
--hidden Include hidden projects
--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. Only
used if --email is provided.
--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:
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. Only used if --email is provided.
--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:
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. Only used if --email is provided.
--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:
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. Only used if --email is provided.
--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:
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. Only used if --email is provided.
--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:
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
--hidden Include hidden projects
--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. Only
used if --email is provided.
--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:
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. Only used if --email is
provided.
--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:
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. Only
used if --email is provided.
--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:
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. Only used if --email is provided.
--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 unhide¶
Unhide projects.
PROJECT_IDS: comma-separted list of projects to be unhidden.
Usage:
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. Only used if --email is provided.
--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 unhide-samples¶
Unhide samples in a project.
PROJECT_ID: Gencove project ID
Usage:
Options:
--sample-ids TEXT A comma separated list of sample ids which will be
hidden.
--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. Only used if --email is
provided.
--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:
Options:
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:
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. Only used if
--email is provided.
--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:
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. Only used if
--email is provided.
--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/base/analysis/fastq-files/uploading-using-s3/
Usage:
Options:
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:
Options:
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:
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. Only used if
--email is provided.
--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:
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. Only used if --email is provided.
--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:
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. Only used if
--email is provided.
--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:
Options:
Subcommands
- get-sample-manifest: Download a sample manifest to a specified destination directory.
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:
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. Only used if --email is provided.
--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:
Options:
Subcommands
- download-file: Download a single sample file. Using this command, sample file can be
- get-metadata: Get sample metadata.
- set-metadata: Set sample metadata.
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:
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. Only used if --email is provided.
--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:
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. Only used if
--email is provided.
--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:
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. Only used if --email is provided.
--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:
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. Only used if
--email is provided.
--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:
Options:
Subcommands
- list: List user uploads.
gencove uploads list¶
List user uploads.
Usage:
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. Only
used if --email is provided.
--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:
Options:
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:
Options: