5 title: "arv subcommands"
9 Copyright (C) The Arvados Authors. All rights reserved.
11 SPDX-License-Identifier: CC-BY-SA-3.0
14 _In order to use the @arv@ command, make sure that you have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html_
16 h3(#arv-create). arv create
18 @arv create@ can be used to create Arvados objects from the command line. Arv create opens up the editor of your choice (set the EDITOR environment variable) and allows you to type or paste a json or yaml description. When saved the object will be created on the API server, if it passes validation.
22 $ <code class="userinput">arv create --help</code>
24 --project-uuid, -p <s>: Project uuid in which to create the object
25 --help, -h: Show this message
31 @arv get@ can be used to get a textual representation of Arvados objects from the command line. The output can be limited to a subset of the object's fields. This command can be used with only the knowledge of an object's UUID.
35 $ <code class="userinput">arv get --help</code>
36 Usage: arv [--format json|yaml] get [uuid] [fields...]
38 Fetch the specified Arvados object, select the specified fields,
39 and print a text representation.
43 h3(#arv-edit). arv edit
45 @arv edit@ can be used to edit Arvados objects from the command line. Arv edit opens up the editor of your choice (set the EDITOR environment variable) with the json or yaml description of the object. Saving the file will update the Arvados object on the API server, if it passes validation.
49 $ <code class="userinput">arv edit --help</code>
50 Arvados command line client
51 Usage: arv edit [uuid] [fields...]
53 Fetch the specified Arvados object, select the specified fields,
54 open an interactive text editor on a text representation (json or
55 yaml, use --format) and then update the object. Will use 'nano'
56 by default, customize with the EDITOR or VISUAL environment variable.
60 h3(#arv-copy). arv copy
62 @arv copy@ can be used to copy a pipeline instance, template or collection from one Arvados instance to another. It takes care of copying the object and all its dependencies.
66 $ <code class="userinput">arv copy --help</code>
67 usage: arv_copy.py [-h] [-v] [--progress] [--no-progress] [-f] --src
68 SOURCE_ARVADOS --dst DESTINATION_ARVADOS [--recursive]
69 [--no-recursive] [--dst-git-repo DST_GIT_REPO]
70 [--project-uuid PROJECT_UUID] [--retries RETRIES]
73 Copy a pipeline instance, template or collection from one Arvados instance to
77 object_uuid The UUID of the object to be copied.
80 -h, --help show this help message and exit
81 -v, --verbose Verbose output.
82 --progress Report progress on copying collections. (default)
83 --no-progress Do not report progress on copying collections.
84 -f, --force Perform copy even if the object appears to exist at
85 the remote destination.
86 --src SOURCE_ARVADOS The name of the source Arvados instance (required) -
87 points at an Arvados config file. May be either a
88 pathname to a config file, or (for example) "foo" as
89 shorthand for $HOME/.config/arvados/foo.conf.
90 --dst DESTINATION_ARVADOS
91 The name of the destination Arvados instance
92 (required) - points at an Arvados config file. May be
93 either a pathname to a config file, or (for example)
94 "foo" as shorthand for $HOME/.config/arvados/foo.conf.
95 --recursive Recursively copy any dependencies for this object.
97 --no-recursive Do not copy any dependencies. NOTE: if this option is
98 given, the copied object will need to be updated
99 manually in order to be functional.
100 --dst-git-repo DST_GIT_REPO
101 The name of the destination git repository. Required
102 when copying a pipeline recursively.
103 --project-uuid PROJECT_UUID
104 The UUID of the project at the destination to which
105 the pipeline should be copied.
106 --retries RETRIES Maximum number of times to retry server requests that
107 encounter temporary failures (e.g., server down).
112 h3(#arv-tag). arv tag
114 @arv tag@ is used to tag Arvados objects.
118 $ <code class="userinput">arv tag --help</code>
121 arv tag add tag1 [tag2 ...] --object object_uuid1 [object_uuid2...]
122 arv tag remove tag1 [tag2 ...] --object object_uuid1 [object_uuid2...]
125 --dry-run, -n: Don't actually do anything
126 --verbose, -v: Print some things on stderr
127 --uuid, -u: Return the UUIDs of the objects in the response, one per
129 --json, -j: Return the entire response received from the API server, as
131 --human, -h: Return the response received from the API server, as a JSON
132 object with whitespace added for human consumption
133 --pretty, -p: Synonym of --human
134 --yaml, -y: Return the response received from the API server, in YAML
136 --help, -e: Show this message
143 @arv ws@ provides access to the websockets event stream.
147 $ <code class="userinput">arv ws --help</code>
148 usage: arv-ws [-h] [-u UUID] [-f FILTERS]
149 [--poll-interval POLL_INTERVAL | --no-poll]
150 [-p PIPELINE | -j JOB]
153 -h, --help show this help message and exit
154 -u UUID, --uuid UUID Filter events on object_uuid
155 -f FILTERS, --filters FILTERS
156 Arvados query filter to apply to log events (JSON
158 --poll-interval POLL_INTERVAL
159 If websockets is not available, specify the polling
160 interval, default is every 15 seconds
161 --no-poll Do not poll if websockets are not available, just fail
162 -p PIPELINE, --pipeline PIPELINE
163 Supply pipeline uuid, print log output from pipeline
165 -j JOB, --job JOB Supply job uuid, print log output from jobs
169 h3(#arv-keep). arv keep
171 @arv keep@ provides access to the Keep storage service.
175 $ <code class="userinput">arv keep --help</code>
176 Usage: arv keep [method] [--parameters]
177 Use 'arv keep [method] --help' to get more information about specific methods.
179 Available methods: ls, get, put, docker
183 h3(#arv-keep-ls). arv keep ls
187 $ <code class="userinput">arv keep ls --help</code>
188 usage: arv-ls [-h] [--retries RETRIES] [-s] locator
190 List contents of a manifest
192 positional arguments:
193 locator Collection UUID or locator
196 -h, --help show this help message and exit
197 --retries RETRIES Maximum number of times to retry server requests that
198 encounter temporary failures (e.g., server down). Default
200 -s List file sizes, in KiB.
204 h3(#arv-keep-get). arv keep get
208 $ <code class="userinput">arv keep get --help</code>
209 usage: arv-get [-h] [--retries RETRIES]
210 [--progress | --no-progress | --batch-progress]
211 [--hash HASH | --md5sum] [-n] [-r] [-f | --skip-existing]
212 locator [destination]
214 Copy data from Keep to a local file or pipe.
216 positional arguments:
217 locator Collection locator, optionally with a file path or
219 destination Local file or directory where the data is to be written.
220 Default: /dev/stdout.
223 -h, --help show this help message and exit
224 --retries RETRIES Maximum number of times to retry server requests that
225 encounter temporary failures (e.g., server down). Default
227 --progress Display human-readable progress on stderr (bytes and, if
228 possible, percentage of total data size). This is the
229 default behavior when it is not expected to interfere
230 with the output: specifically, stderr is a tty _and_
231 either stdout is not a tty, or output is being written to
232 named files rather than stdout.
233 --no-progress Do not display human-readable progress on stderr.
234 --batch-progress Display machine-readable progress on stderr (bytes and,
235 if known, total data size).
236 --hash HASH Display the hash of each file as it is read from Keep,
237 using the given hash algorithm. Supported algorithms
238 include md5, sha1, sha224, sha256, sha384, and sha512.
239 --md5sum Display the MD5 hash of each file as it is read from
241 -n Do not write any data -- just read from Keep, and report
242 md5sums if requested.
243 -r Retrieve all files in the specified collection/prefix.
244 This is the default behavior if the "locator" argument
245 ends with a forward slash.
246 -f Overwrite existing files while writing. The default
247 behavior is to refuse to write *anything* if any of the
248 output files already exist. As a special case, -f is not
249 needed to write to /dev/stdout.
250 --skip-existing Skip files that already exist. The default behavior is to
251 refuse to write *anything* if any files exist that would
252 have to be overwritten. This option causes even devices,
253 sockets, and fifos to be skipped.
257 h3(#arv-keep-put). arv keep put
261 $ <code class="userinput">arv keep put --help</code>
262 usage: arv-put [-h] [--max-manifest-depth N | --normalize]
263 [--as-stream | --stream | --as-manifest | --in-manifest | --manifest | --as-raw | --raw]
264 [--use-filename FILENAME] [--filename FILENAME]
265 [--portable-data-hash] [--replication N]
266 [--project-uuid UUID] [--name NAME]
267 [--progress | --no-progress | --batch-progress]
268 [--resume | --no-resume] [--retries RETRIES]
271 Copy data from the local filesystem to Keep.
273 positional arguments:
274 path Local file or directory. Default: read from standard
278 -h, --help show this help message and exit
279 --max-manifest-depth N
280 Maximum depth of directory tree to represent in the
281 manifest structure. A directory structure deeper than
282 this will be represented as a single stream in the
283 manifest. If N=0, the manifest will contain a single
284 stream. Default: -1 (unlimited), i.e., exactly one
285 manifest stream per filesystem directory that contains
287 --normalize Normalize the manifest by re-ordering files and
288 streams after writing data.
289 --as-stream Synonym for --stream.
290 --stream Store the file content and display the resulting
291 manifest on stdout. Do not write the manifest to Keep
292 or save a Collection object in Arvados.
293 --as-manifest Synonym for --manifest.
294 --in-manifest Synonym for --manifest.
295 --manifest Store the file data and resulting manifest in Keep,
296 save a Collection object in Arvados, and display the
297 manifest locator (Collection uuid) on stdout. This is
298 the default behavior.
299 --as-raw Synonym for --raw.
300 --raw Store the file content and display the data block
301 locators on stdout, separated by commas, with a
302 trailing newline. Do not store a manifest.
303 --use-filename FILENAME
304 Synonym for --filename.
305 --filename FILENAME Use the given filename in the manifest, instead of the
306 name of the local file. This is useful when "-" or
307 "/dev/stdin" is given as an input file. It can be used
308 only if there is exactly one path given and it is not
309 a directory. Implies --manifest.
310 --portable-data-hash Print the portable data hash instead of the Arvados
311 UUID for the collection created by the upload.
312 --replication N Set the replication level for the new collection: how
313 many different physical storage devices (e.g., disks)
314 should have a copy of each data block. Default is to
315 use the server-provided default (if any) or 2.
316 --project-uuid UUID Store the collection in the specified project, instead
317 of your Home project.
318 --name NAME Save the collection with the specified name.
319 --progress Display human-readable progress on stderr (bytes and,
320 if possible, percentage of total data size). This is
321 the default behavior when stderr is a tty.
322 --no-progress Do not display human-readable progress on stderr, even
324 --batch-progress Display machine-readable progress on stderr (bytes
325 and, if known, total data size).
326 --resume Continue interrupted uploads from cached state
328 --no-resume Do not continue interrupted uploads from cached state.
329 --retries RETRIES Maximum number of times to retry server requests that
330 encounter temporary failures (e.g., server down).
336 h3(#arv-pipeline-run). arv pipeline run
338 @arv pipeline run@ can be used to start a pipeline run from the command line.
340 The User Guide has a page with a bit more information on "using arv pipeline run":{{site.baseurl}}/user/topics/running-pipeline-command-line.html.
344 $ <code class="userinput">arv pipeline run --help</code>
346 --dry-run, -n: Do not start any new jobs or wait for existing jobs to
347 finish. Just find out whether jobs are finished,
348 queued, or running for each component.
349 --status-text <s>: Store plain text status in given file. (Default:
351 --status-json <s>: Store json-formatted pipeline in given file. (Default:
353 --no-wait: Do not wait for jobs to finish. Just look up status,
354 submit new jobs if needed, and exit.
355 --no-reuse: Do not reuse existing jobs to satisfy pipeline
356 components. Submit a new job for every component.
357 --debug, -d: Print extra debugging information on stderr.
358 --debug-level <i>: Set debug verbosity level.
359 --template <s>: UUID of pipeline template, or path to local pipeline
361 --instance <s>: UUID of pipeline instance.
362 --submit: Submit the pipeline instance to the server, and exit.
363 Let the Crunch dispatch service satisfy the components
364 by finding/running jobs.
365 --run-pipeline-here: Manage the pipeline instance in-process. Submit jobs
366 to Crunch as needed. Do not exit until the pipeline
368 --run-jobs-here: Run jobs in the local terminal session instead of
369 submitting them to Crunch. Implies
370 --run-pipeline-here. Note: this results in a
371 significantly different job execution environment, and
372 some Crunch features are not supported. It can be
373 necessary to modify a pipeline in order to make it run
375 --run-here: Synonym for --run-jobs-here.
376 --description <s>: Description for the pipeline instance.
377 --version, -v: Print version and exit
378 --help, -h: Show this message
382 h3(#arv-run). arv run
384 The @arv-run@ command creates Arvados pipelines at the command line that fan out to multiple concurrent tasks across Arvados compute nodes.
386 The User Guide has a page on "using arv-run":{{site.baseurl}}/user/topics/arv-run.html.
390 $ <code class="userinput">arv run --help</code>
391 usage: arv-run [-h] [--retries RETRIES] [--dry-run] [--local]
392 [--docker-image DOCKER_IMAGE] [--ignore-rcode] [--no-reuse]
393 [--no-wait] [--project-uuid PROJECT_UUID] [--git-dir GIT_DIR]
394 [--repository REPOSITORY] [--script-version SCRIPT_VERSION]
397 positional arguments:
401 -h, --help show this help message and exit
402 --retries RETRIES Maximum number of times to retry server requests that
403 encounter temporary failures (e.g., server down).
405 --dry-run Print out the pipeline that would be submitted and
407 --local Run locally using arv-run-pipeline-instance
408 --docker-image DOCKER_IMAGE
409 Docker image to use, otherwise use instance default.
410 --ignore-rcode Commands that return non-zero return codes should not
411 be considered failed.
412 --no-reuse Do not reuse past jobs.
413 --no-wait Do not wait and display logs after submitting command,
415 --project-uuid PROJECT_UUID
416 Parent project of the pipeline
417 --git-dir GIT_DIR Git repository passed to arv-crunch-job when using
419 --repository REPOSITORY
420 repository field of component, default 'arvados'
421 --script-version SCRIPT_VERSION
422 script_version field of component, default 'master'