genomics library

Classes

Disk
A Google Compute Engine disk resource specification.
DiskResponse
A Google Compute Engine disk resource specification.
DockerExecutor
The Docker execuctor specification.
DockerExecutorResponse
The Docker execuctor specification.
GetPipelineArgs
Arguments for getPipeline. Arguments for getPipeline.
GetPipelineResult
Result data returned by getPipeline.
LocalCopy
LocalCopy defines how a remote file should be copied to and from the VM.
LocalCopyResponse
LocalCopy defines how a remote file should be copied to and from the VM.
Pipeline
Creates a pipeline that can be run later. Create takes a Pipeline that has all fields other than pipelineId populated, and then returns the same pipeline with pipelineId populated. This id can be used to run the pipeline. Caller must have WRITE permission to the project.
PipelineArgs
The set of arguments for Pipeline. The set of arguments for Pipeline.
PipelineParameter
Parameters facilitate setting and delivering data into the pipeline's execution environment. They are defined at create time, with optional defaults, and can be overridden at run time. If localCopy is unset, then the parameter specifies a string that is passed as-is into the pipeline, as the value of the environment variable with the given name. A default value can be optionally specified at create time. The default can be overridden at run time using the inputs map. If no default is given, a value must be supplied at runtime. If localCopy is defined, then the parameter specifies a data source or sink, both in Google Cloud Storage and on the Docker container where the pipeline computation is run. The service account associated with the Pipeline (by default the project's Compute Engine service account) must have access to the Google Cloud Storage paths. At run time, the Google Cloud Storage paths can be overridden if a default was provided at create time, or must be set otherwise. The pipeline runner should add a key/value pair to either the inputs or outputs map. The indicated data copies will be carried out before/after pipeline execution, just as if the corresponding arguments were provided to gsutil cp. For example: Given the following PipelineParameter, specified in the inputParameters list: {name: "input_file", localCopy: {path: "file.txt", disk: "pd1"}} where disk is defined in the PipelineResources object as: {name: "pd1", mountPoint: "/mnt/disk/"} We create a disk named pd1, mount it on the host VM, and map /mnt/pd1 to /mnt/disk in the docker container. At runtime, an entry for input_file would be required in the inputs map, such as: inputs["input_file"] = "gs://my-bucket/bar.txt" This would generate the following gsutil call: gsutil cp gs://my-bucket/bar.txt /mnt/pd1/file.txt The file /mnt/pd1/file.txt maps to /mnt/disk/file.txt in the Docker container. Acceptable paths are: Google Cloud storage pathLocal path file file glob directory For outputs, the direction of the copy is reversed: gsutil cp /mnt/disk/file.txt gs://my-bucket/bar.txt Acceptable paths are: Local pathGoogle Cloud Storage path file file file directory - directory must already exist glob directory - directory will be created if it doesn't exist One restriction due to docker limitations, is that for outputs that are found on the boot disk, the local path cannot be a glob and must be a file.
PipelineParameterResponse
Parameters facilitate setting and delivering data into the pipeline's execution environment. They are defined at create time, with optional defaults, and can be overridden at run time. If localCopy is unset, then the parameter specifies a string that is passed as-is into the pipeline, as the value of the environment variable with the given name. A default value can be optionally specified at create time. The default can be overridden at run time using the inputs map. If no default is given, a value must be supplied at runtime. If localCopy is defined, then the parameter specifies a data source or sink, both in Google Cloud Storage and on the Docker container where the pipeline computation is run. The service account associated with the Pipeline (by default the project's Compute Engine service account) must have access to the Google Cloud Storage paths. At run time, the Google Cloud Storage paths can be overridden if a default was provided at create time, or must be set otherwise. The pipeline runner should add a key/value pair to either the inputs or outputs map. The indicated data copies will be carried out before/after pipeline execution, just as if the corresponding arguments were provided to gsutil cp. For example: Given the following PipelineParameter, specified in the inputParameters list: {name: "input_file", localCopy: {path: "file.txt", disk: "pd1"}} where disk is defined in the PipelineResources object as: {name: "pd1", mountPoint: "/mnt/disk/"} We create a disk named pd1, mount it on the host VM, and map /mnt/pd1 to /mnt/disk in the docker container. At runtime, an entry for input_file would be required in the inputs map, such as: inputs["input_file"] = "gs://my-bucket/bar.txt" This would generate the following gsutil call: gsutil cp gs://my-bucket/bar.txt /mnt/pd1/file.txt The file /mnt/pd1/file.txt maps to /mnt/disk/file.txt in the Docker container. Acceptable paths are: Google Cloud storage pathLocal path file file glob directory For outputs, the direction of the copy is reversed: gsutil cp /mnt/disk/file.txt gs://my-bucket/bar.txt Acceptable paths are: Local pathGoogle Cloud Storage path file file file directory - directory must already exist glob directory - directory will be created if it doesn't exist One restriction due to docker limitations, is that for outputs that are found on the boot disk, the local path cannot be a glob and must be a file.
PipelineResources
The system resources for the pipeline run.
PipelineResourcesResponse
The system resources for the pipeline run.

Enums

DiskType
Required. The type of the disk to create.

Functions

getPipeline(GetPipelineArgs args, {InvokeOptions? options}) → Future<GetPipelineResult>
Retrieves a pipeline based on ID. Caller must have READ permission to the project. args Arguments passed to this invoke. Arguments for getPipeline. options Invoke options controlling this call.