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| <h1><a href="genomics_v2alpha1.html">Genomics API</a> . <a href="genomics_v2alpha1.pipelines.html">pipelines</a></h1> |
| <h2>Instance Methods</h2> |
| <p class="toc_element"> |
| <code><a href="#run">run(body=None, x__xgafv=None)</a></code></p> |
| <p class="firstline">Runs a pipeline. The returned Operation's metadata field will contain a</p> |
| <h3>Method Details</h3> |
| <div class="method"> |
| <code class="details" id="run">run(body=None, x__xgafv=None)</code> |
| <pre>Runs a pipeline. The returned Operation's metadata field will contain a |
| google.genomics.v2alpha1.Metadata object describing the status of the |
| pipeline execution. The [response] field will contain a |
| google.genomics.v2alpha1.RunPipelineResponse object if the pipeline |
| completes successfully. |
| |
| **Note:** Before you can use this method, the Genomics Service Agent |
| must have access to your project. This is done automatically when the |
| Cloud Genomics API is first enabled, but if you delete this permission, |
| or if you enabled the Cloud Genomics API before the v2alpha1 API |
| launch, you must disable and re-enable the API to grant the Genomics |
| Service Agent the required permissions. |
| Authorization requires the following [Google |
| IAM](https://cloud.google.com/iam/) permission: |
| |
| * `genomics.operations.create` |
| |
| [1]: /genomics/gsa |
| |
| Args: |
| body: object, The request body. |
| The object takes the form of: |
| |
| { # The arguments to the `RunPipeline` method. The requesting user must have |
| # the `iam.serviceAccounts.actAs` permission for the Cloud Genomics service |
| # account or the request will fail. |
| "labels": { # User-defined labels to associate with the returned operation. These |
| # labels are not propagated to any Google Cloud Platform resources used by |
| # the operation, and can be modified at any time. |
| # |
| # To associate labels with resources created while executing the operation, |
| # see the appropriate resource message (for example, `VirtualMachine`). |
| "a_key": "A String", |
| }, |
| "pipeline": { # Specifies a series of actions to execute, expressed as Docker containers. # Required. The description of the pipeline to run. |
| "environment": { # The environment to pass into every action. Each action can also specify |
| # additional environment variables but cannot delete an entry from this map |
| # (though they can overwrite it with a different value). |
| "a_key": "A String", |
| }, |
| "actions": [ # The list of actions to execute, in the order they are specified. |
| { # Specifies a single action that runs a Docker container. |
| "mounts": [ # A list of mounts to make available to the action. |
| # |
| # In addition to the values specified here, every action has a special |
| # virtual disk mounted under `/google` that contains log files and other |
| # operational components. |
| # |
| # <ul> |
| # <li><code>/google/logs</code> All logs written during the pipeline |
| # execution.</li> |
| # <li><code>/google/logs/output</code> The combined standard output and |
| # standard error of all actions run as part of the pipeline |
| # execution.</li> |
| # <li><code>/google/logs/action/*/stdout</code> The complete contents of |
| # each individual action's standard output.</li> |
| # <li><code>/google/logs/action/*/stderr</code> The complete contents of |
| # each individual action's standard error output.</li> |
| # </ul> |
| { # Carries information about a particular disk mount inside a container. |
| "path": "A String", # The path to mount the disk inside the container. |
| "disk": "A String", # The name of the disk to mount, as specified in the resources section. |
| "readOnly": True or False, # If true, the disk is mounted read-only inside the container. |
| }, |
| ], |
| "commands": [ # If specified, overrides the `CMD` specified in the container. If the |
| # container also has an `ENTRYPOINT` the values are used as entrypoint |
| # arguments. Otherwise, they are used as a command and arguments to run |
| # inside the container. |
| "A String", |
| ], |
| "entrypoint": "A String", # If specified, overrides the `ENTRYPOINT` specified in the container. |
| "flags": [ # The set of flags to apply to this action. |
| "A String", |
| ], |
| "credentials": { # Holds encrypted information that is only decrypted and stored in RAM # If the specified image is hosted on a private registry other than Google |
| # Container Registry, the credentials required to pull the image must be |
| # specified here as an encrypted secret. |
| # |
| # The secret must decrypt to a JSON-encoded dictionary containing both |
| # `username` and `password` keys. |
| # by the worker VM when running the pipeline. |
| "cipherText": "A String", # The value of the cipherText response from the `encrypt` method. This field |
| # is intentionally unaudited. |
| "keyName": "A String", # The name of the Cloud KMS key that will be used to decrypt the secret |
| # value. The VM service account must have the required permissions and |
| # authentication scopes to invoke the `decrypt` method on the specified key. |
| }, |
| "labels": { # Labels to associate with the action. This field is provided to assist |
| # workflow engine authors in identifying actions (for example, to indicate |
| # what sort of action they perform, such as localization or debugging). |
| # They are returned in the operation metadata, but are otherwise ignored. |
| "a_key": "A String", |
| }, |
| "timeout": "A String", # The maximum amount of time to give the action to complete. If the action |
| # fails to complete before the timeout, it will be terminated and the exit |
| # status will be non-zero. The pipeline will continue or terminate based |
| # on the rules defined by the `ALWAYS_RUN` and `IGNORE_EXIT_STATUS` flags. |
| "portMappings": { # A map of containers to host port mappings for this container. If the |
| # container already specifies exposed ports, use the |
| # `PUBLISH_EXPOSED_PORTS` flag instead. |
| # |
| # The host port number must be less than 65536. If it is zero, an unused |
| # random port is assigned. To determine the resulting port number, consult |
| # the `ContainerStartedEvent` in the operation metadata. |
| "a_key": 42, |
| }, |
| "environment": { # The environment to pass into the container. This environment is merged |
| # with values specified in the google.genomics.v2alpha1.Pipeline |
| # message, overwriting any duplicate values. |
| # |
| # In addition to the values passed here, a few other values are |
| # automatically injected into the environment. These cannot be hidden or |
| # overwritten. |
| # |
| # `GOOGLE_PIPELINE_FAILED` will be set to "1" if the pipeline failed |
| # because an action has exited with a non-zero status (and did not have the |
| # `IGNORE_EXIT_STATUS` flag set). This can be used to determine if additional |
| # debug or logging actions should execute. |
| # |
| # `GOOGLE_LAST_EXIT_STATUS` will be set to the exit status of the last |
| # non-background action that executed. This can be used by workflow engine |
| # authors to determine whether an individual action has succeeded or failed. |
| "a_key": "A String", |
| }, |
| "name": "A String", # An optional name for the container. The container hostname will be set to |
| # this name, making it useful for inter-container communication. The name |
| # must contain only upper and lowercase alphanumeric characters and hypens |
| # and cannot start with a hyphen. |
| "imageUri": "A String", # Required. The URI to pull the container image from. Note that all images referenced |
| # by actions in the pipeline are pulled before the first action runs. If |
| # multiple actions reference the same image, it is only pulled once, |
| # ensuring that the same image is used for all actions in a single pipeline. |
| # |
| # The image URI can be either a complete host and image specification (e.g., |
| # quay.io/biocontainers/samtools), a library and image name (e.g., |
| # google/cloud-sdk) or a bare image name ('bash') to pull from the default |
| # library. No schema is required in any of these cases. |
| # |
| # If the specified image is not public, the service account specified for |
| # the Virtual Machine must have access to pull the images from GCR, or |
| # appropriate credentials must be specified in the |
| # google.genomics.v2alpha1.Action.credentials field. |
| "pidNamespace": "A String", # An optional identifier for a PID namespace to run the action inside. |
| # Multiple actions should use the same string to share a namespace. If |
| # unspecified, a separate isolated namespace is used. |
| }, |
| ], |
| "resources": { # The system resources for the pipeline run. # The resources required for execution. |
| # |
| # At least one zone or region must be specified or the pipeline run will fail. |
| "regions": [ # The list of regions allowed for VM allocation. If set, the `zones` field |
| # must not be set. |
| "A String", |
| ], |
| "zones": [ # The list of zones allowed for VM allocation. If set, the `regions` field |
| # must not be set. |
| "A String", |
| ], |
| "virtualMachine": { # Carries information about a Compute Engine VM resource. # The virtual machine specification. |
| "preemptible": True or False, # If true, allocate a preemptible VM. |
| "bootDiskSizeGb": 42, # The size of the boot disk, in GB. The boot disk must be large |
| # enough to accommodate all of the Docker images from each action in the |
| # pipeline at the same time. If not specified, a small but reasonable |
| # default value is used. |
| "nvidiaDriverVersion": "A String", # The NVIDIA driver version to use when attaching an NVIDIA GPU accelerator. |
| # The version specified here must be compatible with the GPU libraries |
| # contained in the container being executed, and must be one of the drivers |
| # hosted in the `nvidia-drivers-us-public` bucket on Google Cloud Storage. |
| "labels": { # Optional set of labels to apply to the VM and any attached disk resources. |
| # These labels must adhere to the [name and value |
| # restrictions](https://cloud.google.com/compute/docs/labeling-resources) on |
| # VM labels imposed by Compute Engine. |
| # |
| # Labels keys with the prefix 'google-' are reserved for use by Google. |
| # |
| # Labels applied at creation time to the VM. Applied on a best-effort basis |
| # to attached disk resources shortly after VM creation. |
| "a_key": "A String", |
| }, |
| "bootImage": "A String", # The host operating system image to use. |
| # |
| # Currently, only Container-Optimized OS images can be used. |
| # |
| # The default value is `projects/cos-cloud/global/images/family/cos-stable`, |
| # which selects the latest stable release of Container-Optimized OS. |
| # |
| # This option is provided to allow testing against the beta release of the |
| # operating system to ensure that the new version does not interact |
| # negatively with production pipelines. |
| # |
| # To test a pipeline against the beta release of Container-Optimized OS, |
| # use the value `projects/cos-cloud/global/images/family/cos-beta`. |
| "network": { # VM networking options. # The VM network configuration. |
| "usePrivateAddress": True or False, # If set to true, do not attach a public IP address to the VM. Note that |
| # without a public IP address, additional configuration is required to |
| # allow the VM to access Google services. |
| # |
| # See https://cloud.google.com/vpc/docs/configure-private-google-access |
| # for more information. |
| "subnetwork": "A String", # If the specified network is configured for custom subnet creation, the |
| # name of the subnetwork to attach the instance to must be specified here. |
| # |
| # The value is prefixed with `regions/*/subnetworks/` unless it contains a |
| # `/`, in which case it is assumed to be a fully specified subnetwork |
| # resource URL. |
| # |
| # If the `*` character appears in the value, it is replaced with the region |
| # that the virtual machine has been allocated in. |
| "name": "A String", # The network name to attach the VM's network interface to. The value will |
| # be prefixed with `global/networks/` unless it contains a `/`, in which |
| # case it is assumed to be a fully specified network resource URL. |
| # |
| # If unspecified, the global default network is used. |
| }, |
| "enableStackdriverMonitoring": True or False, # Whether Stackdriver monitoring should be enabled on the VM. |
| "dockerCacheImages": [ # The Compute Engine Disk Images to use as a Docker cache. The disks will be |
| # mounted into the Docker folder in a way that the images present in the |
| # cache will not need to be pulled. The digests of the cached images must |
| # match those of the tags used or the latest version will still be pulled. |
| # Only a single image is supported. |
| "A String", |
| ], |
| "machineType": "A String", # Required. The machine type of the virtual machine to create. Must be the short name |
| # of a standard machine type (such as "n1-standard-1") or a custom machine |
| # type (such as "custom-1-4096", where "1" indicates the number of vCPUs and |
| # "4096" indicates the memory in MB). See |
| # [Creating an instance with a custom machine |
| # type](https://cloud.google.com/compute/docs/instances/creating-instance-with-custom-machine-type#create) |
| # for more specifications on creating a custom machine type. |
| "serviceAccount": { # Carries information about a Google Cloud service account. # The service account to install on the VM. This account does not need |
| # any permissions other than those required by the pipeline. |
| "scopes": [ # List of scopes to be enabled for this service account on the VM, in |
| # addition to the cloud-platform API scope that will be added by default. |
| "A String", |
| ], |
| "email": "A String", # Email address of the service account. If not specified, the default |
| # Compute Engine service account for the project will be used. |
| }, |
| "disks": [ # The list of disks to create and attach to the VM. |
| { # Carries information about a disk that can be attached to a VM. |
| # |
| # See https://cloud.google.com/compute/docs/disks/performance for more |
| # information about disk type, size, and performance considerations. |
| "type": "A String", # The Compute Engine disk type. If unspecified, `pd-standard` is used. |
| "sourceImage": "A String", # An optional image to put on the disk before attaching it to the VM. |
| "sizeGb": 42, # The size, in GB, of the disk to attach. If the size is not |
| # specified, a default is chosen to ensure reasonable I/O performance. |
| # |
| # If the disk type is specified as `local-ssd`, multiple local drives are |
| # automatically combined to provide the requested size. Note, however, that |
| # each physical SSD is 375GB in size, and no more than 8 drives can be |
| # attached to a single instance. |
| "name": "A String", # A user-supplied name for the disk. Used when mounting the disk into |
| # actions. The name must contain only upper and lowercase alphanumeric |
| # characters and hypens and cannot start with a hyphen. |
| }, |
| ], |
| "accelerators": [ # The list of accelerators to attach to the VM. |
| { # Carries information about an accelerator that can be attached to a VM. |
| "type": "A String", # The accelerator type string (for example, "nvidia-tesla-k80"). |
| # |
| # Only NVIDIA GPU accelerators are currently supported. If an NVIDIA GPU is |
| # attached, the required runtime libraries will be made available to all |
| # containers under `/usr/local/nvidia`. The driver version to install must |
| # be specified using the NVIDIA driver version parameter on the virtual |
| # machine specification. Note that attaching a GPU increases the worker VM |
| # startup time by a few minutes. |
| "count": "A String", # How many accelerators of this type to attach. |
| }, |
| ], |
| "cpuPlatform": "A String", # The CPU platform to request. An instance based on a newer platform can be |
| # allocated, but never one with fewer capabilities. The value of this |
| # parameter must be a valid Compute Engine CPU platform name (such as "Intel |
| # Skylake"). This parameter is only useful for carefully optimized work |
| # loads where the CPU platform has a significant impact. |
| # |
| # For more information about the effect of this parameter, see |
| # https://cloud.google.com/compute/docs/instances/specify-min-cpu-platform. |
| }, |
| "projectId": "A String", # The project ID to allocate resources in. |
| }, |
| "timeout": "A String", # The maximum amount of time to give the pipeline to complete. This includes |
| # the time spent waiting for a worker to be allocated. If the pipeline fails |
| # to complete before the timeout, it will be cancelled and the error code |
| # will be set to DEADLINE_EXCEEDED. |
| # |
| # If unspecified, it will default to 7 days. |
| }, |
| } |
| |
| x__xgafv: string, V1 error format. |
| Allowed values |
| 1 - v1 error format |
| 2 - v2 error format |
| |
| Returns: |
| An object of the form: |
| |
| { # This resource represents a long-running operation that is the result of a |
| # network API call. |
| "metadata": { # An OperationMetadata or Metadata object. This will always be returned with the Operation. |
| "a_key": "", # Properties of the object. Contains field @type with type URL. |
| }, |
| "response": { # An Empty object. |
| "a_key": "", # Properties of the object. Contains field @type with type URL. |
| }, |
| "name": "A String", # The server-assigned name, which is only unique within the same service that originally returns it. For example&#58; `operations/CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw` |
| "done": True or False, # If the value is `false`, it means the operation is still in progress. |
| # If `true`, the operation is completed, and either `error` or `response` is |
| # available. |
| "error": { # The `Status` type defines a logical error model that is suitable for # The error result of the operation in case of failure or cancellation. |
| # different programming environments, including REST APIs and RPC APIs. It is |
| # used by [gRPC](https://github.com/grpc). Each `Status` message contains |
| # three pieces of data: error code, error message, and error details. |
| # |
| # You can find out more about this error model and how to work with it in the |
| # [API Design Guide](https://cloud.google.com/apis/design/errors). |
| "message": "A String", # A developer-facing error message, which should be in English. Any |
| # user-facing error message should be localized and sent in the |
| # google.rpc.Status.details field, or localized by the client. |
| "details": [ # A list of messages that carry the error details. There is a common set of |
| # message types for APIs to use. |
| { |
| "a_key": "", # Properties of the object. Contains field @type with type URL. |
| }, |
| ], |
| "code": 42, # The status code, which should be an enum value of google.rpc.Code. |
| }, |
| }</pre> |
| </div> |
| |
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