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161 lines
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161 lines
9.9 KiB
Markdown
<!---
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DO NOT EDIT !
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This file was generated automatically from 'src/mako/cli/README.md.mako'
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DO NOT EDIT !
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-->
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The `genomics1-beta2` command-line interface *(CLI)* allows to use most features of the *Google genomics* service from the comfort of your terminal.
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By default all output is printed to standard out, but flags can be set to direct it into a file independent of your shell's
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capabilities. Errors will be printed to standard error, and cause the program's exit code to be non-zero.
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If data-structures are requested, these will be returned as pretty-printed JSON, to be useful as input to other tools.
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# Usage
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This documentation was generated from the *genomics* API at revision *20150326*. The CLI is at version *0.1.0*.
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```bash
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genomics1-beta2 [options] annotation-sets create -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] annotation-sets delete <annotation-set-id> [-p <v>...]
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genomics1-beta2 [options] annotation-sets get <annotation-set-id> [-p <v>...] [-o <out>]
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genomics1-beta2 [options] annotation-sets patch <annotation-set-id> -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] annotation-sets search -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] annotation-sets update <annotation-set-id> -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] annotations batch-create -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] annotations create -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] annotations delete <annotation-id> [-p <v>...]
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genomics1-beta2 [options] annotations get <annotation-id> [-p <v>...] [-o <out>]
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genomics1-beta2 [options] annotations patch <annotation-id> -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] annotations search -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] annotations update <annotation-id> -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] callsets create -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] callsets delete <call-set-id> [-p <v>...]
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genomics1-beta2 [options] callsets get <call-set-id> [-p <v>...] [-o <out>]
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genomics1-beta2 [options] callsets patch <call-set-id> -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] callsets search -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] callsets update <call-set-id> -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] datasets create -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] datasets delete <dataset-id> [-p <v>...]
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genomics1-beta2 [options] datasets get <dataset-id> [-p <v>...] [-o <out>]
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genomics1-beta2 [options] datasets list [-p <v>...] [-o <out>]
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genomics1-beta2 [options] datasets patch <dataset-id> -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] datasets undelete <dataset-id> [-p <v>...] [-o <out>]
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genomics1-beta2 [options] datasets update <dataset-id> -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] experimental jobs-create -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] jobs cancel <job-id> [-p <v>...]
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genomics1-beta2 [options] jobs get <job-id> [-p <v>...] [-o <out>]
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genomics1-beta2 [options] jobs search -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] readgroupsets align -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] readgroupsets call -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] readgroupsets coveragebuckets-list <read-group-set-id> [-p <v>...] [-o <out>]
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genomics1-beta2 [options] readgroupsets delete <read-group-set-id> [-p <v>...]
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genomics1-beta2 [options] readgroupsets export -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] readgroupsets get <read-group-set-id> [-p <v>...] [-o <out>]
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genomics1-beta2 [options] readgroupsets import -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] readgroupsets patch <read-group-set-id> -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] readgroupsets search -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] readgroupsets update <read-group-set-id> -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] reads search -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] references bases-list <reference-id> [-p <v>...] [-o <out>]
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genomics1-beta2 [options] references get <reference-id> [-p <v>...] [-o <out>]
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genomics1-beta2 [options] references search -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] referencesets get <reference-set-id> [-p <v>...] [-o <out>]
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genomics1-beta2 [options] referencesets search -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] streaming-readstore streamreads -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] variants create -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] variants delete <variant-id> [-p <v>...]
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genomics1-beta2 [options] variants get <variant-id> [-p <v>...] [-o <out>]
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genomics1-beta2 [options] variants search -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] variants update <variant-id> -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] variantsets delete <variant-set-id> [-p <v>...]
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genomics1-beta2 [options] variantsets export <variant-set-id> -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] variantsets get <variant-set-id> [-p <v>...] [-o <out>]
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genomics1-beta2 [options] variantsets import-variants <variant-set-id> -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] variantsets merge-variants <variant-set-id> -r <kv>... [-p <v>...]
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genomics1-beta2 [options] variantsets patch <variant-set-id> -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] variantsets search -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 [options] variantsets update <variant-set-id> -r <kv>... [-p <v>...] [-o <out>]
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genomics1-beta2 --help
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All documentation details can be found at
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http://byron.github.io/google-apis-rs/google_genomics1_beta2_cli/index.html
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Configuration:
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--scope <url>
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Specify the authentication a method should be executed in. Each scope
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requires the user to grant this application permission to use it.
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If unset, it defaults to the shortest scope url for a particular method.
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--config-dir <folder>
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A directory into which we will store our persistent data. Defaults to
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a user-writable directory that we will create during the first invocation.
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[default: ~/.google-service-cli]
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--debug
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Output all server communication to standard error. `tx` and `rx` are placed
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into the same stream.
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--debug-auth
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Output all communication related to authentication to standard error. `tx`
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and `rx` are placed into the same stream.
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```
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# Configuration
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The program will store all persistent data in the `~/.google-service-cli` directory in *JSON* files prefixed with `genomics1-beta2-`. You can change the directory used to store configuration with the `--config-dir` flag on a per-invocation basis.
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More information about the various kinds of persistent data are given in the following paragraphs.
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# Authentication
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Most APIs require a user to authenticate any request. If this is the case, the [scope][scopes] determines the
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set of permissions granted. The granularity of these is usually no more than *read-only* or *full-access*.
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If not set, the system will automatically select the smallest feasible scope, e.g. when invoking a
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method that is read-only, it will ask only for a read-only scope.
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You may use the `--scope` flag to specify a scope directly.
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All applicable scopes are documented in the respective method's CLI documentation.
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The first time a scope is used, the user is asked for permission. Follow the instructions given
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by the CLI to grant permissions, or to decline.
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If a scope was authenticated by the user, the respective information will be stored as *JSON* in the configuration
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directory, e.g. `~/.google-service-cli/genomics1-beta2-token-<scope-hash>.json`. No manual management of these tokens
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is necessary.
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To revoke granted authentication, please refer to the [official documentation][revoke-access].
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# Application Secrets
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In order to allow any application to use Google services, it will need to be registered using the
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[Google Developer Console][google-dev-console]. APIs the application may use are then enabled for it
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one by one. Most APIs can be used for free and have a daily quota.
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To allow more comfortable usage of the CLI without forcing anyone to register an own application, the CLI
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comes with a default application secret that is configured accordingly. This also means that heavy usage
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all around the world may deplete the daily quota.
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You can workaround this limitation by putting your own secrets file at this location:
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`~/.google-service-cli/genomics1-beta2-secret.json`, assuming that the required *genomics* API
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was enabled for it. Such a secret file can be downloaded in the *Google Developer Console* at
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*APIs & auth -> Credentials -> Download JSON* and used as is.
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Learn more about how to setup Google projects and enable APIs using the [official documentation][google-project-new].
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# Debugging
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Even though the CLI does its best to provide usable error messages, sometimes it might be desirable to know
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what exactly led to a particular issue. This is done by allowing all client-server communication to be
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output to standard error *as-is*.
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The `--debug` flag will print all client-server communication to standard error, whereas the `--debug-auth` flag
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will cause all communication related to authentication to standard error.
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If the `--debug` flag is set, error-results will be debug-printed, possibly yielding more information about the
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issue at hand.
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You may consider redirecting standard error into a file for ease of use, e.g. `genomics1-beta2 --debug <resource> <method> [options] 2>debug.txt`.
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[scopes]: https://developers.google.com/+/api/oauth#scopes
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[revoke-access]: http://webapps.stackexchange.com/a/30849
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[google-dev-console]: https://console.developers.google.com/
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[google-project-new]: https://developers.google.com/console/help/new/ |