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75<h1><a href="genomics_v2alpha1.html">Genomics API</a> . <a href="genomics_v2alpha1.pipelines.html">pipelines</a></h1>
76<h2>Instance Methods</h2>
77<p class="toc_element">
Dan O'Mearadd494642020-05-01 07:42:23 -070078 <code><a href="#run">run(body=None, x__xgafv=None)</a></code></p>
79<p class="firstline">Runs a pipeline. The returned Operation's metadata field will contain a</p>
Bu Sun Kim715bd7f2019-06-14 16:50:42 -070080<h3>Method Details</h3>
81<div class="method">
Dan O'Mearadd494642020-05-01 07:42:23 -070082 <code class="details" id="run">run(body=None, x__xgafv=None)</code>
Bu Sun Kim65020912020-05-20 12:08:20 -070083 <pre>Runs a pipeline. The returned Operation&#x27;s metadata field will contain a
Dan O'Mearadd494642020-05-01 07:42:23 -070084google.genomics.v2alpha1.Metadata object describing the status of the
85pipeline execution. The [response] field will contain a
86google.genomics.v2alpha1.RunPipelineResponse object if the pipeline
87completes successfully.
Bu Sun Kim715bd7f2019-06-14 16:50:42 -070088
89**Note:** Before you can use this method, the Genomics Service Agent
90must have access to your project. This is done automatically when the
91Cloud Genomics API is first enabled, but if you delete this permission,
92or if you enabled the Cloud Genomics API before the v2alpha1 API
93launch, you must disable and re-enable the API to grant the Genomics
94Service Agent the required permissions.
95Authorization requires the following [Google
96IAM](https://cloud.google.com/iam/) permission:
97
98* `genomics.operations.create`
99
100[1]: /genomics/gsa
101
102Args:
Dan O'Mearadd494642020-05-01 07:42:23 -0700103 body: object, The request body.
Bu Sun Kim715bd7f2019-06-14 16:50:42 -0700104 The object takes the form of:
105
106{ # The arguments to the `RunPipeline` method. The requesting user must have
107 # the `iam.serviceAccounts.actAs` permission for the Cloud Genomics service
108 # account or the request will fail.
Bu Sun Kim65020912020-05-20 12:08:20 -0700109 &quot;labels&quot;: { # User-defined labels to associate with the returned operation. These
110 # labels are not propagated to any Google Cloud Platform resources used by
111 # the operation, and can be modified at any time.
112 #
113 # To associate labels with resources created while executing the operation,
114 # see the appropriate resource message (for example, `VirtualMachine`).
115 &quot;a_key&quot;: &quot;A String&quot;,
116 },
117 &quot;pipeline&quot;: { # Specifies a series of actions to execute, expressed as Docker containers. # Required. The description of the pipeline to run.
118 &quot;actions&quot;: [ # The list of actions to execute, in the order they are specified.
Dan O'Mearadd494642020-05-01 07:42:23 -0700119 { # Specifies a single action that runs a Docker container.
Bu Sun Kim65020912020-05-20 12:08:20 -0700120 &quot;timeout&quot;: &quot;A String&quot;, # The maximum amount of time to give the action to complete. If the action
121 # fails to complete before the timeout, it will be terminated and the exit
122 # status will be non-zero. The pipeline will continue or terminate based
123 # on the rules defined by the `ALWAYS_RUN` and `IGNORE_EXIT_STATUS` flags.
Bu Sun Kim65020912020-05-20 12:08:20 -0700124 &quot;credentials&quot;: { # Holds encrypted information that is only decrypted and stored in RAM # If the specified image is hosted on a private registry other than Google
125 # Container Registry, the credentials required to pull the image must be
126 # specified here as an encrypted secret.
127 #
128 # The secret must decrypt to a JSON-encoded dictionary containing both
129 # `username` and `password` keys.
130 # by the worker VM when running the pipeline.
131 &quot;keyName&quot;: &quot;A String&quot;, # The name of the Cloud KMS key that will be used to decrypt the secret
132 # value. The VM service account must have the required permissions and
133 # authentication scopes to invoke the `decrypt` method on the specified key.
134 &quot;cipherText&quot;: &quot;A String&quot;, # The value of the cipherText response from the `encrypt` method. This field
135 # is intentionally unaudited.
Dan O'Mearadd494642020-05-01 07:42:23 -0700136 },
Bu Sun Kim4ed7d3f2020-05-27 12:20:54 -0700137 &quot;name&quot;: &quot;A String&quot;, # An optional name for the container. The container hostname will be set to
138 # this name, making it useful for inter-container communication. The name
139 # must contain only upper and lowercase alphanumeric characters and hypens
140 # and cannot start with a hyphen.
Bu Sun Kim65020912020-05-20 12:08:20 -0700141 &quot;imageUri&quot;: &quot;A String&quot;, # Required. The URI to pull the container image from. Note that all images referenced
Dan O'Mearadd494642020-05-01 07:42:23 -0700142 # by actions in the pipeline are pulled before the first action runs. If
143 # multiple actions reference the same image, it is only pulled once,
144 # ensuring that the same image is used for all actions in a single pipeline.
145 #
146 # The image URI can be either a complete host and image specification (e.g.,
147 # quay.io/biocontainers/samtools), a library and image name (e.g.,
Bu Sun Kim65020912020-05-20 12:08:20 -0700148 # google/cloud-sdk) or a bare image name (&#x27;bash&#x27;) to pull from the default
Dan O'Mearadd494642020-05-01 07:42:23 -0700149 # library. No schema is required in any of these cases.
150 #
151 # If the specified image is not public, the service account specified for
152 # the Virtual Machine must have access to pull the images from GCR, or
153 # appropriate credentials must be specified in the
154 # google.genomics.v2alpha1.Action.credentials field.
Bu Sun Kim65020912020-05-20 12:08:20 -0700155 &quot;commands&quot;: [ # If specified, overrides the `CMD` specified in the container. If the
156 # container also has an `ENTRYPOINT` the values are used as entrypoint
157 # arguments. Otherwise, they are used as a command and arguments to run
158 # inside the container.
159 &quot;A String&quot;,
160 ],
161 &quot;flags&quot;: [ # The set of flags to apply to this action.
162 &quot;A String&quot;,
163 ],
Bu Sun Kim65020912020-05-20 12:08:20 -0700164 &quot;portMappings&quot;: { # A map of containers to host port mappings for this container. If the
165 # container already specifies exposed ports, use the
166 # `PUBLISH_EXPOSED_PORTS` flag instead.
167 #
168 # The host port number must be less than 65536. If it is zero, an unused
169 # random port is assigned. To determine the resulting port number, consult
170 # the `ContainerStartedEvent` in the operation metadata.
171 &quot;a_key&quot;: 42,
172 },
173 &quot;environment&quot;: { # The environment to pass into the container. This environment is merged
Dan O'Mearadd494642020-05-01 07:42:23 -0700174 # with values specified in the google.genomics.v2alpha1.Pipeline
175 # message, overwriting any duplicate values.
176 #
177 # In addition to the values passed here, a few other values are
178 # automatically injected into the environment. These cannot be hidden or
179 # overwritten.
180 #
Bu Sun Kim65020912020-05-20 12:08:20 -0700181 # `GOOGLE_PIPELINE_FAILED` will be set to &quot;1&quot; if the pipeline failed
Dan O'Mearadd494642020-05-01 07:42:23 -0700182 # because an action has exited with a non-zero status (and did not have the
183 # `IGNORE_EXIT_STATUS` flag set). This can be used to determine if additional
184 # debug or logging actions should execute.
185 #
186 # `GOOGLE_LAST_EXIT_STATUS` will be set to the exit status of the last
187 # non-background action that executed. This can be used by workflow engine
188 # authors to determine whether an individual action has succeeded or failed.
Bu Sun Kim65020912020-05-20 12:08:20 -0700189 &quot;a_key&quot;: &quot;A String&quot;,
Dan O'Mearadd494642020-05-01 07:42:23 -0700190 },
Bu Sun Kim4ed7d3f2020-05-27 12:20:54 -0700191 &quot;labels&quot;: { # Labels to associate with the action. This field is provided to assist
192 # workflow engine authors in identifying actions (for example, to indicate
193 # what sort of action they perform, such as localization or debugging).
194 # They are returned in the operation metadata, but are otherwise ignored.
195 &quot;a_key&quot;: &quot;A String&quot;,
196 },
Bu Sun Kim65020912020-05-20 12:08:20 -0700197 &quot;entrypoint&quot;: &quot;A String&quot;, # If specified, overrides the `ENTRYPOINT` specified in the container.
198 &quot;pidNamespace&quot;: &quot;A String&quot;, # An optional identifier for a PID namespace to run the action inside.
199 # Multiple actions should use the same string to share a namespace. If
200 # unspecified, a separate isolated namespace is used.
201 &quot;mounts&quot;: [ # A list of mounts to make available to the action.
Dan O'Mearadd494642020-05-01 07:42:23 -0700202 #
203 # In addition to the values specified here, every action has a special
204 # virtual disk mounted under `/google` that contains log files and other
205 # operational components.
206 #
207 # &lt;ul&gt;
208 # &lt;li&gt;&lt;code&gt;/google/logs&lt;/code&gt; All logs written during the pipeline
209 # execution.&lt;/li&gt;
210 # &lt;li&gt;&lt;code&gt;/google/logs/output&lt;/code&gt; The combined standard output and
211 # standard error of all actions run as part of the pipeline
212 # execution.&lt;/li&gt;
213 # &lt;li&gt;&lt;code&gt;/google/logs/action/*/stdout&lt;/code&gt; The complete contents of
Bu Sun Kim65020912020-05-20 12:08:20 -0700214 # each individual action&#x27;s standard output.&lt;/li&gt;
Dan O'Mearadd494642020-05-01 07:42:23 -0700215 # &lt;li&gt;&lt;code&gt;/google/logs/action/*/stderr&lt;/code&gt; The complete contents of
Bu Sun Kim65020912020-05-20 12:08:20 -0700216 # each individual action&#x27;s standard error output.&lt;/li&gt;
Dan O'Mearadd494642020-05-01 07:42:23 -0700217 # &lt;/ul&gt;
218 { # Carries information about a particular disk mount inside a container.
Bu Sun Kim65020912020-05-20 12:08:20 -0700219 &quot;path&quot;: &quot;A String&quot;, # The path to mount the disk inside the container.
220 &quot;disk&quot;: &quot;A String&quot;, # The name of the disk to mount, as specified in the resources section.
221 &quot;readOnly&quot;: True or False, # If true, the disk is mounted read-only inside the container.
Dan O'Mearadd494642020-05-01 07:42:23 -0700222 },
223 ],
Dan O'Mearadd494642020-05-01 07:42:23 -0700224 },
225 ],
Bu Sun Kim65020912020-05-20 12:08:20 -0700226 &quot;environment&quot;: { # The environment to pass into every action. Each action can also specify
227 # additional environment variables but cannot delete an entry from this map
228 # (though they can overwrite it with a different value).
229 &quot;a_key&quot;: &quot;A String&quot;,
230 },
231 &quot;timeout&quot;: &quot;A String&quot;, # The maximum amount of time to give the pipeline to complete. This includes
232 # the time spent waiting for a worker to be allocated. If the pipeline fails
233 # to complete before the timeout, it will be cancelled and the error code
234 # will be set to DEADLINE_EXCEEDED.
235 #
236 # If unspecified, it will default to 7 days.
237 &quot;resources&quot;: { # The system resources for the pipeline run. # The resources required for execution.
238 #
239 # At least one zone or region must be specified or the pipeline run will fail.
240 &quot;projectId&quot;: &quot;A String&quot;, # The project ID to allocate resources in.
241 &quot;regions&quot;: [ # The list of regions allowed for VM allocation. If set, the `zones` field
242 # must not be set.
243 &quot;A String&quot;,
244 ],
245 &quot;zones&quot;: [ # The list of zones allowed for VM allocation. If set, the `regions` field
246 # must not be set.
247 &quot;A String&quot;,
248 ],
249 &quot;virtualMachine&quot;: { # Carries information about a Compute Engine VM resource. # The virtual machine specification.
Bu Sun Kim4ed7d3f2020-05-27 12:20:54 -0700250 &quot;cpuPlatform&quot;: &quot;A String&quot;, # The CPU platform to request. An instance based on a newer platform can be
251 # allocated, but never one with fewer capabilities. The value of this
252 # parameter must be a valid Compute Engine CPU platform name (such as &quot;Intel
253 # Skylake&quot;). This parameter is only useful for carefully optimized work
254 # loads where the CPU platform has a significant impact.
255 #
256 # For more information about the effect of this parameter, see
257 # https://cloud.google.com/compute/docs/instances/specify-min-cpu-platform.
258 &quot;accelerators&quot;: [ # The list of accelerators to attach to the VM.
259 { # Carries information about an accelerator that can be attached to a VM.
260 &quot;count&quot;: &quot;A String&quot;, # How many accelerators of this type to attach.
261 &quot;type&quot;: &quot;A String&quot;, # The accelerator type string (for example, &quot;nvidia-tesla-k80&quot;).
262 #
263 # Only NVIDIA GPU accelerators are currently supported. If an NVIDIA GPU is
264 # attached, the required runtime libraries will be made available to all
265 # containers under `/usr/local/nvidia`. The driver version to install must
266 # be specified using the NVIDIA driver version parameter on the virtual
267 # machine specification. Note that attaching a GPU increases the worker VM
268 # startup time by a few minutes.
269 },
270 ],
271 &quot;machineType&quot;: &quot;A String&quot;, # Required. The machine type of the virtual machine to create. Must be the short name
272 # of a standard machine type (such as &quot;n1-standard-1&quot;) or a custom machine
273 # type (such as &quot;custom-1-4096&quot;, where &quot;1&quot; indicates the number of vCPUs and
274 # &quot;4096&quot; indicates the memory in MB). See
275 # [Creating an instance with a custom machine
276 # type](https://cloud.google.com/compute/docs/instances/creating-instance-with-custom-machine-type#create)
277 # for more specifications on creating a custom machine type.
Bu Sun Kim65020912020-05-20 12:08:20 -0700278 &quot;preemptible&quot;: True or False, # If true, allocate a preemptible VM.
279 &quot;disks&quot;: [ # The list of disks to create and attach to the VM.
280 { # Carries information about a disk that can be attached to a VM.
281 #
282 # See https://cloud.google.com/compute/docs/disks/performance for more
283 # information about disk type, size, and performance considerations.
Bu Sun Kim65020912020-05-20 12:08:20 -0700284 &quot;sourceImage&quot;: &quot;A String&quot;, # An optional image to put on the disk before attaching it to the VM.
285 &quot;sizeGb&quot;: 42, # The size, in GB, of the disk to attach. If the size is not
286 # specified, a default is chosen to ensure reasonable I/O performance.
287 #
288 # If the disk type is specified as `local-ssd`, multiple local drives are
289 # automatically combined to provide the requested size. Note, however, that
290 # each physical SSD is 375GB in size, and no more than 8 drives can be
291 # attached to a single instance.
Bu Sun Kim4ed7d3f2020-05-27 12:20:54 -0700292 &quot;name&quot;: &quot;A String&quot;, # A user-supplied name for the disk. Used when mounting the disk into
293 # actions. The name must contain only upper and lowercase alphanumeric
294 # characters and hypens and cannot start with a hyphen.
295 &quot;type&quot;: &quot;A String&quot;, # The Compute Engine disk type. If unspecified, `pd-standard` is used.
Bu Sun Kim65020912020-05-20 12:08:20 -0700296 },
297 ],
298 &quot;bootImage&quot;: &quot;A String&quot;, # The host operating system image to use.
299 #
300 # Currently, only Container-Optimized OS images can be used.
301 #
302 # The default value is `projects/cos-cloud/global/images/family/cos-stable`,
303 # which selects the latest stable release of Container-Optimized OS.
304 #
305 # This option is provided to allow testing against the beta release of the
306 # operating system to ensure that the new version does not interact
307 # negatively with production pipelines.
308 #
309 # To test a pipeline against the beta release of Container-Optimized OS,
310 # use the value `projects/cos-cloud/global/images/family/cos-beta`.
311 &quot;serviceAccount&quot;: { # Carries information about a Google Cloud service account. # The service account to install on the VM. This account does not need
312 # any permissions other than those required by the pipeline.
313 &quot;email&quot;: &quot;A String&quot;, # Email address of the service account. If not specified, the default
314 # Compute Engine service account for the project will be used.
315 &quot;scopes&quot;: [ # List of scopes to be enabled for this service account on the VM, in
316 # addition to the cloud-platform API scope that will be added by default.
317 &quot;A String&quot;,
318 ],
319 },
320 &quot;network&quot;: { # VM networking options. # The VM network configuration.
321 &quot;name&quot;: &quot;A String&quot;, # The network name to attach the VM&#x27;s network interface to. The value will
322 # be prefixed with `global/networks/` unless it contains a `/`, in which
323 # case it is assumed to be a fully specified network resource URL.
324 #
325 # If unspecified, the global default network is used.
326 &quot;usePrivateAddress&quot;: True or False, # If set to true, do not attach a public IP address to the VM. Note that
327 # without a public IP address, additional configuration is required to
328 # allow the VM to access Google services.
329 #
330 # See https://cloud.google.com/vpc/docs/configure-private-google-access
331 # for more information.
332 &quot;subnetwork&quot;: &quot;A String&quot;, # If the specified network is configured for custom subnet creation, the
333 # name of the subnetwork to attach the instance to must be specified here.
334 #
335 # The value is prefixed with `regions/*/subnetworks/` unless it contains a
336 # `/`, in which case it is assumed to be a fully specified subnetwork
337 # resource URL.
338 #
339 # If the `*` character appears in the value, it is replaced with the region
340 # that the virtual machine has been allocated in.
341 },
342 &quot;bootDiskSizeGb&quot;: 42, # The size of the boot disk, in GB. The boot disk must be large
343 # enough to accommodate all of the Docker images from each action in the
344 # pipeline at the same time. If not specified, a small but reasonable
345 # default value is used.
346 &quot;nvidiaDriverVersion&quot;: &quot;A String&quot;, # The NVIDIA driver version to use when attaching an NVIDIA GPU accelerator.
347 # The version specified here must be compatible with the GPU libraries
348 # contained in the container being executed, and must be one of the drivers
349 # hosted in the `nvidia-drivers-us-public` bucket on Google Cloud Storage.
350 &quot;labels&quot;: { # Optional set of labels to apply to the VM and any attached disk resources.
351 # These labels must adhere to the [name and value
352 # restrictions](https://cloud.google.com/compute/docs/labeling-resources) on
353 # VM labels imposed by Compute Engine.
354 #
355 # Labels keys with the prefix &#x27;google-&#x27; are reserved for use by Google.
356 #
357 # Labels applied at creation time to the VM. Applied on a best-effort basis
358 # to attached disk resources shortly after VM creation.
359 &quot;a_key&quot;: &quot;A String&quot;,
360 },
361 &quot;enableStackdriverMonitoring&quot;: True or False, # Whether Stackdriver monitoring should be enabled on the VM.
Bu Sun Kim65020912020-05-20 12:08:20 -0700362 },
363 },
Bu Sun Kim715bd7f2019-06-14 16:50:42 -0700364 },
365 }
366
367 x__xgafv: string, V1 error format.
368 Allowed values
369 1 - v1 error format
370 2 - v2 error format
371
372Returns:
373 An object of the form:
374
375 { # This resource represents a long-running operation that is the result of a
376 # network API call.
Bu Sun Kim4ed7d3f2020-05-27 12:20:54 -0700377 &quot;metadata&quot;: { # An OperationMetadata or Metadata object. This will always be returned with the Operation.
378 &quot;a_key&quot;: &quot;&quot;, # Properties of the object. Contains field @type with type URL.
379 },
380 &quot;done&quot;: True or False, # If the value is `false`, it means the operation is still in progress.
381 # If `true`, the operation is completed, and either `error` or `response` is
382 # available.
Bu Sun Kim65020912020-05-20 12:08:20 -0700383 &quot;response&quot;: { # An Empty object.
384 &quot;a_key&quot;: &quot;&quot;, # Properties of the object. Contains field @type with type URL.
Dan O'Mearadd494642020-05-01 07:42:23 -0700385 },
Bu Sun Kim65020912020-05-20 12:08:20 -0700386 &quot;name&quot;: &quot;A String&quot;, # The server-assigned name, which is only unique within the same service that originally returns it. For example&amp;#58; `operations/CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw`
387 &quot;error&quot;: { # The `Status` type defines a logical error model that is suitable for # The error result of the operation in case of failure or cancellation.
Bu Sun Kim715bd7f2019-06-14 16:50:42 -0700388 # different programming environments, including REST APIs and RPC APIs. It is
389 # used by [gRPC](https://github.com/grpc). Each `Status` message contains
390 # three pieces of data: error code, error message, and error details.
391 #
392 # You can find out more about this error model and how to work with it in the
393 # [API Design Guide](https://cloud.google.com/apis/design/errors).
Bu Sun Kim65020912020-05-20 12:08:20 -0700394 &quot;code&quot;: 42, # The status code, which should be an enum value of google.rpc.Code.
395 &quot;message&quot;: &quot;A String&quot;, # A developer-facing error message, which should be in English. Any
Bu Sun Kim715bd7f2019-06-14 16:50:42 -0700396 # user-facing error message should be localized and sent in the
397 # google.rpc.Status.details field, or localized by the client.
Bu Sun Kim65020912020-05-20 12:08:20 -0700398 &quot;details&quot;: [ # A list of messages that carry the error details. There is a common set of
Bu Sun Kim715bd7f2019-06-14 16:50:42 -0700399 # message types for APIs to use.
400 {
Bu Sun Kim65020912020-05-20 12:08:20 -0700401 &quot;a_key&quot;: &quot;&quot;, # Properties of the object. Contains field @type with type URL.
Bu Sun Kim715bd7f2019-06-14 16:50:42 -0700402 },
403 ],
404 },
Bu Sun Kim715bd7f2019-06-14 16:50:42 -0700405 }</pre>
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