.TH "GCLOUD_ALPHA_GENOMICS_PIPELINES_RUN" 1



.SH "NAME"
.HP
gcloud alpha genomics pipelines run \- defines and runs a pipeline



.SH "SYNOPSIS"
.HP
\f5gcloud alpha genomics pipelines run\fR [\fB\-\-command\-line\fR=\fICOMMAND_LINE\fR] [\fB\-\-cpus\fR=\fICPUS\fR] [\fB\-\-disk\-size\fR=\fIDISK_SIZE\fR] [\fB\-\-docker\-image\fR=\fIDOCKER_IMAGE\fR;\ default="google/cloud\-sdk:slim"] [\fB\-\-env\-vars\fR=[\fINAME\fR=\fIVALUE\fR,...]] [\fB\-\-inputs\fR=[\fINAME\fR=\fIVALUE\fR,...]] [\fB\-\-inputs\-from\-file\fR=[\fINAME\fR=\fIFILE\fR,...]] [\fB\-\-logging\fR=\fILOGGING\fR] [\fB\-\-memory\fR=\fIMEMORY\fR] [\fB\-\-outputs\fR=[\fINAME\fR=\fIVALUE\fR,...]] [\fB\-\-preemptible\fR] [\fB\-\-boot\-disk\-size\fR=\fIBOOT_DISK_SIZE\fR] [\fB\-\-labels\fR=[\fIKEY\fR=\fIVALUE\fR,...]] [\fB\-\-network\fR=\fINETWORK\fR] [\fB\-\-pipeline\-file\fR=\fIPIPELINE_FILE\fR] [\fB\-\-regions\fR=[\fIREGION\fR,...]] [\fB\-\-service\-account\-email\fR=\fISERVICE_ACCOUNT_EMAIL\fR;\ default="default"] [\fB\-\-service\-account\-scopes\fR=[\fISCOPE\fR,...]] [\fB\-\-subnetwork\fR=\fISUBNETWORK\fR] [\fB\-\-zones\fR=[\fIZONE\fR,...]] [\fIGCLOUD_WIDE_FLAG\ ...\fR]



.SH "DESCRIPTION"

\fB(ALPHA)\fR A pipeline is a transformation of a set of inputs to a set of
outputs. Supports docker\-based commands.



.SH "COMMONLY USED FLAGS"

.RS 2m
.TP 2m
\fB\-\-command\-line\fR=\fICOMMAND_LINE\fR

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

.TP 2m
\fB\-\-cpus\fR=\fICPUS\fR

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

.TP 2m
\fB\-\-disk\-size\fR=\fIDISK_SIZE\fR

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

.TP 2m
\fB\-\-docker\-image\fR=\fIDOCKER_IMAGE\fR; default="google/cloud\-sdk:slim"

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

.TP 2m
\fB\-\-env\-vars\fR=[\fINAME\fR=\fIVALUE\fR,...]

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

.TP 2m
\fB\-\-inputs\fR=[\fINAME\fR=\fIVALUE\fR,...]

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

.TP 2m
\fB\-\-inputs\-from\-file\fR=[\fINAME\fR=\fIFILE\fR,...]

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

.TP 2m
\fB\-\-logging\fR=\fILOGGING\fR

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 be
output with a unique identifier as the filename in that directory, or as a fully
specified path, which must end in \f5.log\fR, in which case that path will be
used. Stdout and stderr logs from the run are also generated and output as
\f5\-stdout.log\fR and \f5\-stderr.log\fR.

.TP 2m
\fB\-\-memory\fR=\fIMEMORY\fR

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

.TP 2m
\fB\-\-outputs\fR=[\fINAME\fR=\fIVALUE\fR,...]

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

.TP 2m
\fB\-\-preemptible\fR

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


.RE
.sp

.SH "OTHER FLAGS"

.RS 2m
.TP 2m
\fB\-\-boot\-disk\-size\fR=\fIBOOT_DISK_SIZE\fR

The size of the boot disk in GB.

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

.TP 2m
\fB\-\-labels\fR=[\fIKEY\fR=\fIVALUE\fR,...]

List of label KEY=VALUE pairs to add.

Keys must start with a lowercase character and contain only hyphens (\f5\-\fR),
underscores (\f5_\fR), lowercase characters, and numbers. Values must contain
only hyphens (\f5\-\fR), underscores (\f5_\fR), lowercase characters, and
numbers.

.TP 2m
\fB\-\-network\fR=\fINETWORK\fR

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.

.TP 2m
\fB\-\-pipeline\-file\fR=\fIPIPELINE_FILE\fR

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

.TP 2m
\fB\-\-regions\fR=[\fIREGION\fR,...]

List of Compute Engine regions the pipeline can run in.

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

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

At least one region or region must be specified.

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

.TP 2m
\fB\-\-service\-account\-email\fR=\fISERVICE_ACCOUNT_EMAIL\fR; default="default"

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

.TP 2m
\fB\-\-service\-account\-scopes\fR=[\fISCOPE\fR,...]

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

.RS 2m
https://www.googleapis.com/auth/devstorage.read_write
https://www.googleapis.com/auth/genomics
.RE

.TP 2m
\fB\-\-subnetwork\fR=\fISUBNETWORK\fR

The subnetwork to use on the provided network.

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.

.TP 2m
\fB\-\-zones\fR=[\fIZONE\fR,...]

List of Compute Engine zones the pipeline can run in.

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

If no zones are specified in the pipeline definition, then the default zone in
your 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, see
https://cloud.google.com/compute/docs/gcloud\-compute/#set_default_zone_and_region_in_your_local_client


.RE
.sp

.SH "GCLOUD WIDE FLAGS"

These flags are available to all commands: \-\-access\-token\-file, \-\-account,
\-\-billing\-project, \-\-configuration, \-\-flags\-file, \-\-flatten,
\-\-format, \-\-help, \-\-impersonate\-service\-account, \-\-log\-http,
\-\-project, \-\-quiet, \-\-trace\-token, \-\-user\-output\-enabled,
\-\-verbosity.

Run \fB$ gcloud help\fR for details.



.SH "NOTES"

This command is currently in alpha and might change without notice. If this
command fails with API permission errors despite specifying the correct project,
you might be trying to access an API with an invitation\-only early access
allowlist.