gcloud alpha genomics pipelines run - defines and runs a pipeline

gcloud alpha genomics pipelines run[--command-line=COMMAND_LINE][--cpus=CPUS][--disk-size=DISK_SIZE][--docker-image=DOCKER_IMAGE; default="google/cloud-sdk:slim"][--env-vars=[NAME=VALUE,…]][--inputs=[NAME=VALUE,…]][--inputs-from-file=[NAME=FILE,…]][--logging=LOGGING][--memory=MEMORY][--outputs=[NAME=VALUE,…]][--preemptible][--boot-disk-size=BOOT_DISK_SIZE][--labels=[KEY=VALUE,…]][--network=NETWORK][--pipeline-file=PIPELINE_FILE][--regions=[REGION,…]][--service-account-email=SERVICE_ACCOUNT_EMAIL; default="default"][--service-account-scopes=[SCOPE,…]][--subnetwork=SUBNETWORK][--zones=[ZONE,…]][GCLOUD_WIDE_FLAG …]

--command-line=COMMAND_LINE

Command line to run with /bin/sh in the specified docker image. Cannot be usedwith --pipeline-file.

--cpus=CPUS

The minimum number of CPUs to run the pipeline. Overrides any value specified inthe pipeline-file.

--disk-size=DISK_SIZE

The disk size(s) in GB, specified as a comma-separated list of pairs of diskname and size. For example: --disk-size "name:size,name2:size2". Overrides anyvalues specified in the pipeline-file.

--docker-image=DOCKER_IMAGE; default="google/cloud-sdk:slim"

A docker image to run. Requires --command-line to be specified and cannot beused with --pipeline-file.

--env-vars=[NAME=VALUE,…]

List of key-value pairs to set as environment variables.

--inputs=[NAME=VALUE,…]

Map of input PipelineParameter names to values. Used to pass literal parametersto the pipeline, and to specify input files in Google Cloud Storage that willhave a localCopy made. Specified as a comma-separated list: --inputsfile=gs://my-bucket/in.txt,name=hello

--inputs-from-file=[NAME=FILE,…]

Map of input PipelineParameter names to values. Used to pass literal parametersto the pipeline where values come from local files; this can be used to sendlarge pipeline input parameters, such as code, data, or configuration values.Specified as a comma-separated list: --inputs-from-filescript=myshellscript.sh,pyfile=mypython.py

--logging=LOGGING

The location in Google Cloud Storage to which the pipeline logs will be copied.Can be specified as a fully qualified directory path, in which case logs will beoutput with a unique identifier as the filename in that directory, or as a fullyspecified path, which must end in.log, in which case that pathwill be used. Stdout and stderr logs from the run are also generated and outputas-stdout.log and-stderr.log.

--memory=MEMORY

The number of GB of RAM needed to run the pipeline. Overrides any valuespecified in the pipeline-file.

--outputs=[NAME=VALUE,…]

Map of output PipelineParameter names to values. Used to specify output files inGoogle Cloud Storage that will be made from a localCopy. Specified as acomma-separated list: --outputs ref=gs://my-bucket/foo,ref2=gs://my-bucket/bar

--preemptible

Whether to use a preemptible VM for this pipeline. The "resource" section of thepipeline-file must also set preemptible to "true" for this flag to take effect.

--boot-disk-size=BOOT_DISK_SIZE

The size of the boot disk in GB.

The boot disk size must be large enough to accomondate all Docker images fromeach action in the pipeline at the same time. If not specified, a small butreasonable default value is used.

--labels=[KEY=VALUE,…]

List of label KEY=VALUE pairs to add.

Keys must start with a lowercase character and contain only hyphens(-), underscores (_), lowercase characters, andnumbers. Values must contain only hyphens (-), underscores(_), lowercase characters, and numbers.

--network=NETWORK

The network name to attach the VM's network interface to.

The value will be prefixed with global/networks/ unless it contains a /, inwhich case it is assumed to be a fully specified network resource URL.

If unspecified, the global default network is used.

--pipeline-file=PIPELINE_FILE

A YAML or JSON file containing a v2alpha1 Pipeline object. Seehttps://cloud.google.com/genomics/reference/rest/v2alpha1/pipelines#Pipeline

--regions=[REGION,…]

List of Compute Engine regions the pipeline can run in.

If no regions are specified with the regions flag, then regions in the pipelinedefinition file will be used.

If no regions are specified in the pipeline definition, then the default regionin your local client configuration is used.

At least one region or region must be specified.

For more information on default regions, seehttps://cloud.google.com/compute/docs/gcloud-compute/#set_default_zone_and_region_in_your_local_client

--service-account-email=SERVICE_ACCOUNT_EMAIL; default="default"

The service account used to run the pipeline. If unspecified, defaults to theCompute Engine service account for your project.

--service-account-scopes=[SCOPE,…]

List of additional scopes to be made available for this service account. Thefollowing scopes are always requested:

https://www.googleapis.com/auth/devstorage.read_writehttps://www.googleapis.com/auth/genomics

--subnetwork=SUBNETWORK

The subnetwork to use on the provided network.

If the specified network is configured for custom subnet creation, the name ofthe subnetwork to attach the instance to must be specified here.

The value is prefixed with regions/*/subnetworks/ unless it contains a /, inwhich 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 thevirtual machine has been allocated in.

--zones=[ZONE,…]

List of Compute Engine zones the pipeline can run in.

If no zones are specified with the zones flag, then zones in the pipelinedefinition file will be used.

If no zones are specified in the pipeline definition, then the default zone inyour local client configuration is used.

If you have no default zone then at least one zone or region must be specified.

For more information on default zones, seehttps://cloud.google.com/compute/docs/gcloud-compute/#set_default_zone_and_region_in_your_local_client

Run$gcloud help for details.