cloudos-cli 2.23.0__tar.gz → 2.24.0__tar.gz

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Files changed (27) hide show
  1. {cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/PKG-INFO +70 -60
  2. {cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/README.md +69 -59
  3. {cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/cloudos_cli/__main__.py +28 -4
  4. cloudos_cli-2.24.0/cloudos_cli/_version.py +1 -0
  5. {cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/cloudos_cli/jobs/job.py +32 -2
  6. {cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/cloudos_cli.egg-info/PKG-INFO +70 -60
  7. cloudos_cli-2.23.0/cloudos_cli/_version.py +0 -1
  8. {cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/LICENSE +0 -0
  9. {cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/cloudos_cli/__init__.py +0 -0
  10. {cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/cloudos_cli/clos.py +0 -0
  11. {cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/cloudos_cli/configure/__init__.py +0 -0
  12. {cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/cloudos_cli/configure/configure.py +0 -0
  13. {cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/cloudos_cli/jobs/__init__.py +0 -0
  14. {cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/cloudos_cli/queue/__init__.py +0 -0
  15. {cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/cloudos_cli/queue/queue.py +0 -0
  16. {cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/cloudos_cli/utils/__init__.py +0 -0
  17. {cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/cloudos_cli/utils/errors.py +0 -0
  18. {cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/cloudos_cli/utils/requests.py +0 -0
  19. {cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/cloudos_cli.egg-info/SOURCES.txt +0 -0
  20. {cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/cloudos_cli.egg-info/dependency_links.txt +0 -0
  21. {cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/cloudos_cli.egg-info/entry_points.txt +0 -0
  22. {cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/cloudos_cli.egg-info/requires.txt +0 -0
  23. {cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/cloudos_cli.egg-info/top_level.txt +0 -0
  24. {cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/setup.cfg +0 -0
  25. {cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/setup.py +0 -0
  26. {cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/tests/__init__.py +0 -0
  27. {cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/tests/functions_for_pytest.py +0 -0
{cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
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2
  Name: cloudos_cli
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- Version: 2.23.0
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+ Version: 2.24.0
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  Summary: Python package for interacting with CloudOS
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5
  Home-page: https://github.com/lifebit-ai/cloudos-cli
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6
  Author: David Piñeyro
@@ -193,65 +193,75 @@ own subcommands with its own `--help`:
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  cloudos job run --help
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  ```
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  ```console
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- Usage: cloudos job run [OPTIONS]
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-
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- Submit a job to CloudOS.
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-
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- ╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
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- │ * --apikey -k TEXT Your CloudOS API key [required] │
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- │ --cloudos-url -c TEXT The CloudOS url you are trying to access to. Default=https://cloudos.lifebit.ai. │
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- │ * --workspace-id TEXT The specific CloudOS workspace id. [required] │
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- │ * --project-name TEXT The name of a CloudOS project. [required] │
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- │ * --workflow-name TEXT The name of a CloudOS workflow or pipeline. [required] │
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- │ --job-config TEXT A config file similar to a nextflow.config file, but only with the parameters to │
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- │ use with your job. │
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- │ --parameter -p TEXT A single parameter to pass to the job call. It should be in the following form: │
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- │ parameter_name=parameter_value. E.g.: -p input=s3://path_to_my_file. You can use │
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- │ this option as many times as parameters you want to include. │
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- │ --nextflow-profile TEXT A comma separated string indicating the nextflow profile/s to use with your job. │
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- │ --nextflow-version [22.10.8|24.04.4|22.11.1-edge|latest] Nextflow version to use when executing the workflow in CloudOS. Default=22.10.8. │
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- │ --git-commit TEXT The git commit hash to run for the selected pipeline. If not specified it │
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- │ defaults to the last commit of the default branch. │
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- │ --git-tag TEXT The tag to run for the selected pipeline. If not specified it defaults to the │
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- │ last commit of the default branch. │
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- │ --git-branch TEXT The branch to run for the selected pipeline. If not specified it defaults to the │
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- │ last commit of the default branch. │
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- │ --job-name TEXT The name of the job. Default=new_job. │
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- │ --resumable Whether to make the job able to be resumed or not. │
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- │ --do-not-save-logs Avoids process log saving. If you select this option, your job process logs will │
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- │ not be stored. │
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- │ --job-queue TEXT Name of the job queue to use with a batch job. │
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- │ --instance-type TEXT The type of execution platform compute instance to use. │
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- │ Default=c5.xlarge(aws)|Standard_D4as_v4(azure). │
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- │ --instance-disk INTEGER The amount of disk storage to configure. Default=500. │
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- │ --storage-mode TEXT Either 'lustre' or 'regular'. Indicates if the user wants to select regular or │
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- │ lustre storage. Default=regular. │
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- │ --lustre-size INTEGER The lustre storage to be used when --storage-mode=lustre, in GB. It should be │
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- │ 1200 or a multiple of it. Default=1200. │
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- │ --wait-completion Whether to wait to job completion and report final job status. │
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- │ --wait-time INTEGER Max time to wait (in seconds) to job completion. Default=3600. │
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- │ --wdl-mainfile TEXT For WDL workflows, which mainFile (.wdl) is configured to use. │
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- │ --wdl-importsfile TEXT For WDL workflows, which importsFile (.zip) is configured to use. │
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- │ --cromwell-token -t TEXT Specific Cromwell server authentication token. Currently, not necessary as │
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- │ apikey can be used instead, but maintained for backwards compatibility. │
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- │ --repository-platform TEXT Name of the repository platform of the workflow. Default=github. │
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- │ --execution-platform [aws|azure|hpc] Name of the execution platform implemented in your CloudOS. Default=aws. │
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- │ --hpc-id TEXT ID of your HPC, only applicable when --execution-platform=hpc. │
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- │ Default=660fae20f93358ad61e0104b │
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- │ --cost-limit FLOAT Add a cost limit to your job. Default=30.0 (For no cost limit please use -1). │
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- │ --accelerate-file-staging Enables AWS S3 mountpoint for quicker file staging. │
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- │ --use-private-docker-repository Allows to use private docker repository for running jobs. The Docker user │
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- │ account has to be already linked to CloudOS. │
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- │ --verbose Whether to print information messages or not. │
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- │ --request-interval INTEGER Time interval to request (in seconds) the job status. For large jobs is │
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- │ important to use a high number to make fewer requests so that is not considered │
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- │ spamming by the API. Default=30. │
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- │ --disable-ssl-verification Disable SSL certificate verification. Please, remember that this option is not │
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- │ generally recommended for security reasons. │
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- │ --ssl-cert TEXT Path to your SSL certificate file. │
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- │ --profile TEXT Profile to use from the config file │
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- │ --help Show this message and exit. │
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- ╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
196
+ Usage: cloudos job run [OPTIONS]
197
+
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+ Submit a job to CloudOS.
199
+
200
+ ╭─ Options ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
201
+ │ * --apikey -k TEXT Your CloudOS API key [required] │
202
+ │ --cloudos-url -c TEXT The CloudOS url you are trying to access to. │
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+ │ Default=https://cloudos.lifebit.ai. │
204
+ │ * --workspace-id TEXT The specific CloudOS workspace id. [required] │
205
+ │ * --project-name TEXT The name of a CloudOS project. [required] │
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+ │ * --workflow-name TEXT The name of a CloudOS workflow or pipeline. [required] │
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+ │ --job-config TEXT A config file similar to a nextflow.config file, but only with the │
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+ │ parameters to use with your job. │
209
+ │ --parameter -p TEXT A single parameter to pass to the job call. It should be in the following │
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+ │ form: parameter_name=parameter_value. E.g.: -p │
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+ │ input=s3://path_to_my_file. You can use this option as many times as │
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+ │ parameters you want to include. │
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+ │ --nextflow-profile TEXT A comma separated string indicating the nextflow profile/s to use with │
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+ │ your job. │
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+ │ --nextflow-version [22.10.8|24.04.4|22.11.1-edge|latest] Nextflow version to use when executing the workflow in CloudOS. │
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+ │ Default=22.10.8. │
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+ │ --git-commit TEXT The git commit hash to run for the selected pipeline. If not specified it │
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+ │ defaults to the last commit of the default branch. │
219
+ │ --git-tag TEXT The tag to run for the selected pipeline. If not specified it defaults to │
220
+ │ the last commit of the default branch. │
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+ │ --git-branch TEXT The branch to run for the selected pipeline. If not specified it defaults │
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+ │ to the last commit of the default branch. │
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+ │ --job-name TEXT The name of the job. Default=new_job. │
224
+ │ --resumable Whether to make the job able to be resumed or not. │
225
+ │ --do-not-save-logs Avoids process log saving. If you select this option, your job process │
226
+ │ logs will not be stored. │
227
+ │ --job-queue TEXT Name of the job queue to use with a batch job. │
228
+ │ --instance-type TEXT The type of compute instance to use as master node. │
229
+ │ Default=c5.xlarge(aws)|Standard_D4as_v4(azure). │
230
+ │ --instance-disk INTEGER The disk space of the master node instance, in GB. Default=500. │
231
+ │ --storage-mode TEXT Either 'lustre' or 'regular'. Indicates if the user wants to select │
232
+ │ regular or lustre storage. Default=regular. │
233
+ │ --lustre-size INTEGER The lustre storage to be used when --storage-mode=lustre, in GB. It │
234
+ │ should be 1200 or a multiple of it. Default=1200. │
235
+ │ --wait-completion Whether to wait to job completion and report final job status. │
236
+ │ --wait-time INTEGER Max time to wait (in seconds) to job completion. Default=3600. │
237
+ │ --wdl-mainfile TEXT For WDL workflows, which mainFile (.wdl) is configured to use. │
238
+ │ --wdl-importsfile TEXT For WDL workflows, which importsFile (.zip) is configured to use. │
239
+ │ --cromwell-token -t TEXT Specific Cromwell server authentication token. Currently, not necessary │
240
+ │ as apikey can be used instead, but maintained for backwards │
241
+ │ compatibility. │
242
+ │ --repository-platform TEXT Name of the repository platform of the workflow. Default=github. │
243
+ │ --execution-platform [aws|azure|hpc] Name of the execution platform implemented in your CloudOS. Default=aws. │
244
+ │ --hpc-id TEXT ID of your HPC, only applicable when --execution-platform=hpc. │
245
+ │ Default=660fae20f93358ad61e0104b │
246
+ │ --azure-worker-instance-type TEXT The worker node instance type to be used in azure. │
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+ │ Default=Standard_D4as_v4 │
248
+ │ --azure-worker-instance-disk INTEGER The disk size in GB for the worker node to be used in azure. Default=100 │
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+ │ --azure-worker-instance-spot Whether the azure worker nodes have to be spot instances or not. │
250
+ │ --cost-limit FLOAT Add a cost limit to your job. Default=30.0 (For no cost limit please use │
251
+ │ -1). │
252
+ │ --accelerate-file-staging Enables AWS S3 mountpoint for quicker file staging. │
253
+ │ --use-private-docker-repository Allows to use private docker repository for running jobs. The Docker user │
254
+ │ account has to be already linked to CloudOS. │
255
+ │ --verbose Whether to print information messages or not. │
256
+ │ --request-interval INTEGER Time interval to request (in seconds) the job status. For large jobs is │
257
+ │ important to use a high number to make fewer requests so that is not │
258
+ │ considered spamming by the API. Default=30. │
259
+ │ --disable-ssl-verification Disable SSL certificate verification. Please, remember that this option │
260
+ │ is not generally recommended for security reasons. │
261
+ │ --ssl-cert TEXT Path to your SSL certificate file. │
262
+ │ --profile TEXT Profile to use from the config file │
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+ │ --help Show this message and exit. │
264
+ ╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
255
265
  ```
256
266
 
257
267
  #### Send a job to CloudOS
{cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/README.md RENAMED
@@ -158,65 +158,75 @@ own subcommands with its own `--help`:
158
158
  cloudos job run --help
159
159
  ```
160
160
  ```console
161
- Usage: cloudos job run [OPTIONS]
162
-
163
- Submit a job to CloudOS.
164
-
165
- ╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
166
- │ * --apikey -k TEXT Your CloudOS API key [required] │
167
- │ --cloudos-url -c TEXT The CloudOS url you are trying to access to. Default=https://cloudos.lifebit.ai. │
168
- │ * --workspace-id TEXT The specific CloudOS workspace id. [required] │
169
- │ * --project-name TEXT The name of a CloudOS project. [required] │
170
- │ * --workflow-name TEXT The name of a CloudOS workflow or pipeline. [required] │
171
- │ --job-config TEXT A config file similar to a nextflow.config file, but only with the parameters to │
172
- │ use with your job. │
173
- │ --parameter -p TEXT A single parameter to pass to the job call. It should be in the following form: │
174
- │ parameter_name=parameter_value. E.g.: -p input=s3://path_to_my_file. You can use │
175
- │ this option as many times as parameters you want to include. │
176
- │ --nextflow-profile TEXT A comma separated string indicating the nextflow profile/s to use with your job. │
177
- │ --nextflow-version [22.10.8|24.04.4|22.11.1-edge|latest] Nextflow version to use when executing the workflow in CloudOS. Default=22.10.8. │
178
- │ --git-commit TEXT The git commit hash to run for the selected pipeline. If not specified it │
179
- │ defaults to the last commit of the default branch. │
180
- │ --git-tag TEXT The tag to run for the selected pipeline. If not specified it defaults to the │
181
- │ last commit of the default branch. │
182
- │ --git-branch TEXT The branch to run for the selected pipeline. If not specified it defaults to the │
183
- │ last commit of the default branch. │
184
- │ --job-name TEXT The name of the job. Default=new_job. │
185
- │ --resumable Whether to make the job able to be resumed or not. │
186
- │ --do-not-save-logs Avoids process log saving. If you select this option, your job process logs will │
187
- │ not be stored. │
188
- │ --job-queue TEXT Name of the job queue to use with a batch job. │
189
- │ --instance-type TEXT The type of execution platform compute instance to use. │
190
- │ Default=c5.xlarge(aws)|Standard_D4as_v4(azure). │
191
- │ --instance-disk INTEGER The amount of disk storage to configure. Default=500. │
192
- │ --storage-mode TEXT Either 'lustre' or 'regular'. Indicates if the user wants to select regular or │
193
- │ lustre storage. Default=regular. │
194
- │ --lustre-size INTEGER The lustre storage to be used when --storage-mode=lustre, in GB. It should be │
195
- │ 1200 or a multiple of it. Default=1200. │
196
- │ --wait-completion Whether to wait to job completion and report final job status. │
197
- │ --wait-time INTEGER Max time to wait (in seconds) to job completion. Default=3600. │
198
- │ --wdl-mainfile TEXT For WDL workflows, which mainFile (.wdl) is configured to use. │
199
- │ --wdl-importsfile TEXT For WDL workflows, which importsFile (.zip) is configured to use. │
200
- │ --cromwell-token -t TEXT Specific Cromwell server authentication token. Currently, not necessary as │
201
- │ apikey can be used instead, but maintained for backwards compatibility. │
202
- │ --repository-platform TEXT Name of the repository platform of the workflow. Default=github. │
203
- │ --execution-platform [aws|azure|hpc] Name of the execution platform implemented in your CloudOS. Default=aws. │
204
- │ --hpc-id TEXT ID of your HPC, only applicable when --execution-platform=hpc. │
205
- │ Default=660fae20f93358ad61e0104b │
206
- │ --cost-limit FLOAT Add a cost limit to your job. Default=30.0 (For no cost limit please use -1). │
207
- │ --accelerate-file-staging Enables AWS S3 mountpoint for quicker file staging. │
208
- │ --use-private-docker-repository Allows to use private docker repository for running jobs. The Docker user │
209
- │ account has to be already linked to CloudOS. │
210
- │ --verbose Whether to print information messages or not. │
211
- │ --request-interval INTEGER Time interval to request (in seconds) the job status. For large jobs is │
212
- │ important to use a high number to make fewer requests so that is not considered │
213
- │ spamming by the API. Default=30. │
214
- │ --disable-ssl-verification Disable SSL certificate verification. Please, remember that this option is not │
215
- │ generally recommended for security reasons. │
216
- │ --ssl-cert TEXT Path to your SSL certificate file. │
217
- │ --profile TEXT Profile to use from the config file │
218
- │ --help Show this message and exit. │
219
- ╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
161
+ Usage: cloudos job run [OPTIONS]
162
+
163
+ Submit a job to CloudOS.
164
+
165
+ ╭─ Options ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
166
+ │ * --apikey -k TEXT Your CloudOS API key [required] │
167
+ │ --cloudos-url -c TEXT The CloudOS url you are trying to access to. │
168
+ │ Default=https://cloudos.lifebit.ai. │
169
+ │ * --workspace-id TEXT The specific CloudOS workspace id. [required] │
170
+ │ * --project-name TEXT The name of a CloudOS project. [required] │
171
+ │ * --workflow-name TEXT The name of a CloudOS workflow or pipeline. [required] │
172
+ │ --job-config TEXT A config file similar to a nextflow.config file, but only with the │
173
+ │ parameters to use with your job. │
174
+ │ --parameter -p TEXT A single parameter to pass to the job call. It should be in the following │
175
+ │ form: parameter_name=parameter_value. E.g.: -p │
176
+ │ input=s3://path_to_my_file. You can use this option as many times as │
177
+ │ parameters you want to include. │
178
+ │ --nextflow-profile TEXT A comma separated string indicating the nextflow profile/s to use with │
179
+ │ your job. │
180
+ │ --nextflow-version [22.10.8|24.04.4|22.11.1-edge|latest] Nextflow version to use when executing the workflow in CloudOS. │
181
+ │ Default=22.10.8. │
182
+ │ --git-commit TEXT The git commit hash to run for the selected pipeline. If not specified it │
183
+ │ defaults to the last commit of the default branch. │
184
+ │ --git-tag TEXT The tag to run for the selected pipeline. If not specified it defaults to │
185
+ │ the last commit of the default branch. │
186
+ │ --git-branch TEXT The branch to run for the selected pipeline. If not specified it defaults │
187
+ │ to the last commit of the default branch. │
188
+ │ --job-name TEXT The name of the job. Default=new_job. │
189
+ │ --resumable Whether to make the job able to be resumed or not. │
190
+ │ --do-not-save-logs Avoids process log saving. If you select this option, your job process │
191
+ │ logs will not be stored. │
192
+ │ --job-queue TEXT Name of the job queue to use with a batch job. │
193
+ │ --instance-type TEXT The type of compute instance to use as master node. │
194
+ │ Default=c5.xlarge(aws)|Standard_D4as_v4(azure). │
195
+ │ --instance-disk INTEGER The disk space of the master node instance, in GB. Default=500. │
196
+ │ --storage-mode TEXT Either 'lustre' or 'regular'. Indicates if the user wants to select │
197
+ │ regular or lustre storage. Default=regular. │
198
+ │ --lustre-size INTEGER The lustre storage to be used when --storage-mode=lustre, in GB. It │
199
+ │ should be 1200 or a multiple of it. Default=1200. │
200
+ │ --wait-completion Whether to wait to job completion and report final job status. │
201
+ │ --wait-time INTEGER Max time to wait (in seconds) to job completion. Default=3600. │
202
+ │ --wdl-mainfile TEXT For WDL workflows, which mainFile (.wdl) is configured to use. │
203
+ │ --wdl-importsfile TEXT For WDL workflows, which importsFile (.zip) is configured to use. │
204
+ │ --cromwell-token -t TEXT Specific Cromwell server authentication token. Currently, not necessary │
205
+ │ as apikey can be used instead, but maintained for backwards │
206
+ │ compatibility. │
207
+ │ --repository-platform TEXT Name of the repository platform of the workflow. Default=github. │
208
+ │ --execution-platform [aws|azure|hpc] Name of the execution platform implemented in your CloudOS. Default=aws. │
209
+ │ --hpc-id TEXT ID of your HPC, only applicable when --execution-platform=hpc. │
210
+ │ Default=660fae20f93358ad61e0104b │
211
+ │ --azure-worker-instance-type TEXT The worker node instance type to be used in azure. │
212
+ │ Default=Standard_D4as_v4 │
213
+ │ --azure-worker-instance-disk INTEGER The disk size in GB for the worker node to be used in azure. Default=100 │
214
+ │ --azure-worker-instance-spot Whether the azure worker nodes have to be spot instances or not. │
215
+ │ --cost-limit FLOAT Add a cost limit to your job. Default=30.0 (For no cost limit please use │
216
+ │ -1). │
217
+ │ --accelerate-file-staging Enables AWS S3 mountpoint for quicker file staging. │
218
+ │ --use-private-docker-repository Allows to use private docker repository for running jobs. The Docker user │
219
+ │ account has to be already linked to CloudOS. │
220
+ │ --verbose Whether to print information messages or not. │
221
+ │ --request-interval INTEGER Time interval to request (in seconds) the job status. For large jobs is │
222
+ │ important to use a high number to make fewer requests so that is not │
223
+ │ considered spamming by the API. Default=30. │
224
+ │ --disable-ssl-verification Disable SSL certificate verification. Please, remember that this option │
225
+ │ is not generally recommended for security reasons. │
226
+ │ --ssl-cert TEXT Path to your SSL certificate file. │
227
+ │ --profile TEXT Profile to use from the config file │
228
+ │ --help Show this message and exit. │
229
+ ╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
220
230
  ```
221
231
 
222
232
  #### Send a job to CloudOS
{cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/cloudos_cli/__main__.py RENAMED
@@ -266,11 +266,11 @@ def configure(ctx, profile, make_default):
266
266
  @click.option('--job-queue',
267
267
  help='Name of the job queue to use with a batch job.')
268
268
  @click.option('--instance-type',
269
- help=('The type of execution platform compute instance to use. ' +
269
+ help=('The type of compute instance to use as master node. ' +
270
270
  'Default=c5.xlarge(aws)|Standard_D4as_v4(azure).'),
271
271
  default='NONE_SELECTED')
272
272
  @click.option('--instance-disk',
273
- help='The amount of disk storage to configure. Default=500.',
273
+ help='The disk space of the master node instance, in GB. Default=500.',
274
274
  type=int,
275
275
  default=500)
276
276
  @click.option('--storage-mode',
@@ -309,6 +309,17 @@ def configure(ctx, profile, make_default):
309
309
  help=('ID of your HPC, only applicable when --execution-platform=hpc. ' +
310
310
  'Default=660fae20f93358ad61e0104b'),
311
311
  default='660fae20f93358ad61e0104b')
312
+ @click.option('--azure-worker-instance-type',
313
+ help=('The worker node instance type to be used in azure. ' +
314
+ 'Default=Standard_D4as_v4'),
315
+ default='Standard_D4as_v4')
316
+ @click.option('--azure-worker-instance-disk',
317
+ help='The disk size in GB for the worker node to be used in azure. Default=100',
318
+ type=int,
319
+ default=100)
320
+ @click.option('--azure-worker-instance-spot',
321
+ help='Whether the azure worker nodes have to be spot instances or not.',
322
+ is_flag=True)
312
323
  @click.option('--cost-limit',
313
324
  help='Add a cost limit to your job. Default=30.0 (For no cost limit please use -1).',
314
325
  type=float,
@@ -366,6 +377,9 @@ def run(ctx,
366
377
  repository_platform,
367
378
  execution_platform,
368
379
  hpc_id,
380
+ azure_worker_instance_type,
381
+ azure_worker_instance_disk,
382
+ azure_worker_instance_spot,
369
383
  cost_limit,
370
384
  accelerate_file_staging,
371
385
  use_private_docker_repository,
@@ -508,6 +522,12 @@ def run(ctx,
508
522
  'is a CloudOS module. CloudOS modules only work with ' +
509
523
  'Nextflow version 22.10.8. Switching to use 22.10.8')
510
524
  nextflow_version = '22.10.8'
525
+ if execution_platform == 'azure':
526
+ print(f'[Message] The selected worflow \'{workflow_name}\' ' +
527
+ 'is a CloudOS module. For these workflows, worker nodes '+
528
+ 'are managed internally. For this reason, the options '+
529
+ 'azure-worker-instance-type, azure-worker-instance-disk and '+
530
+ 'azure-worker-instance-spot are not taking effect.')
511
531
  else:
512
532
  queue = Queue(cloudos_url=cloudos_url, apikey=apikey, cromwell_token=cromwell_token,
513
533
  workspace_id=workspace_id, verify=verify_ssl)
@@ -563,6 +583,7 @@ def run(ctx,
563
583
  print(f'\tNextflow version: {nextflow_version}')
564
584
  j_id = j.send_job(job_config=job_config,
565
585
  parameter=parameter,
586
+ is_module =is_module,
566
587
  git_commit=git_commit,
567
588
  git_tag=git_tag,
568
589
  git_branch=git_branch,
@@ -581,6 +602,9 @@ def run(ctx,
581
602
  hpc_id=hpc_id,
582
603
  workflow_type=workflow_type,
583
604
  cromwell_id=cromwell_id,
605
+ azure_worker_instance_type=azure_worker_instance_type,
606
+ azure_worker_instance_disk=azure_worker_instance_disk,
607
+ azure_worker_instance_spot=azure_worker_instance_spot,
584
608
  cost_limit=cost_limit,
585
609
  use_mountpoints=use_mountpoints,
586
610
  docker_login=docker_login,
@@ -1611,11 +1635,11 @@ def remove_profile(ctx, profile):
1611
1635
  @click.option('--job-queue',
1612
1636
  help='Name of the job queue to use with a batch job.')
1613
1637
  @click.option('--instance-type',
1614
- help=('The type of execution platform compute instance to use. ' +
1638
+ help=('The type of compute instance to use as master node. ' +
1615
1639
  'Default=c5.xlarge(aws)|Standard_D4as_v4(azure).'),
1616
1640
  default='NONE_SELECTED')
1617
1641
  @click.option('--instance-disk',
1618
- help='The amount of disk storage to configure. Default=500.',
1642
+ help='The disk space of the master node instance, in GB. Default=500.',
1619
1643
  type=int,
1620
1644
  default=500)
1621
1645
  @click.option('--cpus',
cloudos_cli-2.24.0/cloudos_cli/_version.py ADDED
@@ -0,0 +1 @@
1
+ __version__ = '2.24.0'
{cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/cloudos_cli/jobs/job.py RENAMED
@@ -174,6 +174,7 @@ class Job(Cloudos):
174
174
  def convert_nextflow_to_json(self,
175
175
  job_config,
176
176
  parameter,
177
+ is_module,
177
178
  example_parameters,
178
179
  git_commit,
179
180
  git_tag,
@@ -195,6 +196,9 @@ class Job(Cloudos):
195
196
  hpc_id,
196
197
  workflow_type,
197
198
  cromwell_id,
199
+ azure_worker_instance_type,
200
+ azure_worker_instance_disk,
201
+ azure_worker_instance_spot,
198
202
  cost_limit,
199
203
  use_mountpoints,
200
204
  docker_login,
@@ -245,7 +249,7 @@ class Job(Cloudos):
245
249
  instance_type : string
246
250
  Name of the instance type to be used for the job master node, for example for AWS EC2 c5.xlarge
247
251
  instance_disk : int
248
- The disk space of the instance, in GB.
252
+ The disk space of the master node instance, in GB.
249
253
  storage_mode : string
250
254
  Either 'lustre' or 'regular'. Indicates if the user wants to select regular
251
255
  or lustre storage.
@@ -260,6 +264,12 @@ class Job(Cloudos):
260
264
  The type of workflow to run. It could be 'nextflow', 'wdl' or 'docker'.
261
265
  cromwell_id : str
262
266
  Cromwell server ID.
267
+ azure_worker_instance_type: str
268
+ The worker node instance type to be used in azure.
269
+ azure_worker_instance_disk: int
270
+ The disk size in GB for the worker node to be used in azure.
271
+ azure_worker_instance_spot: bool
272
+ Whether the azure worker nodes have to be spot instances or not.
263
273
  cost_limit : float
264
274
  Job cost limit. -1 means no cost limit.
265
275
  use_mountpoints : bool
@@ -422,6 +432,12 @@ class Job(Cloudos):
422
432
  "enabled": batch,
423
433
  "jobQueue": job_queue_id
424
434
  }
435
+ if execution_platform == 'azure' and not is_module:
436
+ params['azureBatch'] = {
437
+ "vmType": azure_worker_instance_type,
438
+ "spot": azure_worker_instance_spot,
439
+ "diskSizeInGb": azure_worker_instance_disk
440
+ }
425
441
  if workflow_type == 'docker':
426
442
  params['command'] = command
427
443
  params["resourceRequirements"] = {
@@ -449,6 +465,7 @@ class Job(Cloudos):
449
465
  def send_job(self,
450
466
  job_config=None,
451
467
  parameter=(),
468
+ is_module=False,
452
469
  example_parameters=[],
453
470
  git_commit=None,
454
471
  git_tag=None,
@@ -468,6 +485,9 @@ class Job(Cloudos):
468
485
  hpc_id=None,
469
486
  workflow_type='nextflow',
470
487
  cromwell_id=None,
488
+ azure_worker_instance_type='Standard_D4as_v4',
489
+ azure_worker_instance_disk=100,
490
+ azure_worker_instance_spot=False,
471
491
  cost_limit=30.0,
472
492
  use_mountpoints=False,
473
493
  docker_login=False,
@@ -515,7 +535,7 @@ class Job(Cloudos):
515
535
  instance_type : string
516
536
  Name of the instance type to be used for the job master node, for example for AWS EC2 c5.xlarge
517
537
  instance_disk : int
518
- The disk space of the instance, in GB.
538
+ The disk space of the master node instance, in GB.
519
539
  storage_mode : string
520
540
  Either 'lustre' or 'regular'. Indicates if the user wants to select regular
521
541
  or lustre storage.
@@ -530,6 +550,12 @@ class Job(Cloudos):
530
550
  The type of workflow to run. It could be 'nextflow', 'wdl' or 'docker'.
531
551
  cromwell_id : str
532
552
  Cromwell server ID.
553
+ azure_worker_instance_type: str
554
+ The worker node instance type to be used in azure.
555
+ azure_worker_instance_disk: int
556
+ The disk size in GB for the worker node to be used in azure.
557
+ azure_worker_instance_spot: bool
558
+ Whether the azure worker nodes have to be spot instances or not.
533
559
  cost_limit : float
534
560
  Job cost limit. -1 means no cost limit.
535
561
  use_mountpoints : bool
@@ -564,6 +590,7 @@ class Job(Cloudos):
564
590
  }
565
591
  params = self.convert_nextflow_to_json(job_config,
566
592
  parameter,
593
+ is_module,
567
594
  example_parameters,
568
595
  git_commit,
569
596
  git_tag,
@@ -585,6 +612,9 @@ class Job(Cloudos):
585
612
  hpc_id,
586
613
  workflow_type,
587
614
  cromwell_id,
615
+ azure_worker_instance_type,
616
+ azure_worker_instance_disk,
617
+ azure_worker_instance_spot,
588
618
  cost_limit,
589
619
  use_mountpoints,
590
620
  docker_login,
{cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/cloudos_cli.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: cloudos_cli
3
- Version: 2.23.0
3
+ Version: 2.24.0
4
4
  Summary: Python package for interacting with CloudOS
5
5
  Home-page: https://github.com/lifebit-ai/cloudos-cli
6
6
  Author: David Piñeyro
@@ -193,65 +193,75 @@ own subcommands with its own `--help`:
193
193
  cloudos job run --help
194
194
  ```
195
195
  ```console
196
- Usage: cloudos job run [OPTIONS]
197
-
198
- Submit a job to CloudOS.
199
-
200
- ╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
201
- │ * --apikey -k TEXT Your CloudOS API key [required] │
202
- │ --cloudos-url -c TEXT The CloudOS url you are trying to access to. Default=https://cloudos.lifebit.ai. │
203
- │ * --workspace-id TEXT The specific CloudOS workspace id. [required] │
204
- │ * --project-name TEXT The name of a CloudOS project. [required] │
205
- │ * --workflow-name TEXT The name of a CloudOS workflow or pipeline. [required] │
206
- │ --job-config TEXT A config file similar to a nextflow.config file, but only with the parameters to │
207
- │ use with your job. │
208
- │ --parameter -p TEXT A single parameter to pass to the job call. It should be in the following form: │
209
- │ parameter_name=parameter_value. E.g.: -p input=s3://path_to_my_file. You can use │
210
- │ this option as many times as parameters you want to include. │
211
- │ --nextflow-profile TEXT A comma separated string indicating the nextflow profile/s to use with your job. │
212
- │ --nextflow-version [22.10.8|24.04.4|22.11.1-edge|latest] Nextflow version to use when executing the workflow in CloudOS. Default=22.10.8. │
213
- │ --git-commit TEXT The git commit hash to run for the selected pipeline. If not specified it │
214
- │ defaults to the last commit of the default branch. │
215
- │ --git-tag TEXT The tag to run for the selected pipeline. If not specified it defaults to the │
216
- │ last commit of the default branch. │
217
- │ --git-branch TEXT The branch to run for the selected pipeline. If not specified it defaults to the │
218
- │ last commit of the default branch. │
219
- │ --job-name TEXT The name of the job. Default=new_job. │
220
- │ --resumable Whether to make the job able to be resumed or not. │
221
- │ --do-not-save-logs Avoids process log saving. If you select this option, your job process logs will │
222
- │ not be stored. │
223
- │ --job-queue TEXT Name of the job queue to use with a batch job. │
224
- │ --instance-type TEXT The type of execution platform compute instance to use. │
225
- │ Default=c5.xlarge(aws)|Standard_D4as_v4(azure). │
226
- │ --instance-disk INTEGER The amount of disk storage to configure. Default=500. │
227
- │ --storage-mode TEXT Either 'lustre' or 'regular'. Indicates if the user wants to select regular or │
228
- │ lustre storage. Default=regular. │
229
- │ --lustre-size INTEGER The lustre storage to be used when --storage-mode=lustre, in GB. It should be │
230
- │ 1200 or a multiple of it. Default=1200. │
231
- │ --wait-completion Whether to wait to job completion and report final job status. │
232
- │ --wait-time INTEGER Max time to wait (in seconds) to job completion. Default=3600. │
233
- │ --wdl-mainfile TEXT For WDL workflows, which mainFile (.wdl) is configured to use. │
234
- │ --wdl-importsfile TEXT For WDL workflows, which importsFile (.zip) is configured to use. │
235
- │ --cromwell-token -t TEXT Specific Cromwell server authentication token. Currently, not necessary as │
236
- │ apikey can be used instead, but maintained for backwards compatibility. │
237
- │ --repository-platform TEXT Name of the repository platform of the workflow. Default=github. │
238
- │ --execution-platform [aws|azure|hpc] Name of the execution platform implemented in your CloudOS. Default=aws. │
239
- │ --hpc-id TEXT ID of your HPC, only applicable when --execution-platform=hpc. │
240
- │ Default=660fae20f93358ad61e0104b │
241
- │ --cost-limit FLOAT Add a cost limit to your job. Default=30.0 (For no cost limit please use -1). │
242
- │ --accelerate-file-staging Enables AWS S3 mountpoint for quicker file staging. │
243
- │ --use-private-docker-repository Allows to use private docker repository for running jobs. The Docker user │
244
- │ account has to be already linked to CloudOS. │
245
- │ --verbose Whether to print information messages or not. │
246
- │ --request-interval INTEGER Time interval to request (in seconds) the job status. For large jobs is │
247
- │ important to use a high number to make fewer requests so that is not considered │
248
- │ spamming by the API. Default=30. │
249
- │ --disable-ssl-verification Disable SSL certificate verification. Please, remember that this option is not │
250
- │ generally recommended for security reasons. │
251
- │ --ssl-cert TEXT Path to your SSL certificate file. │
252
- │ --profile TEXT Profile to use from the config file │
253
- │ --help Show this message and exit. │
254
- ╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
196
+ Usage: cloudos job run [OPTIONS]
197
+
198
+ Submit a job to CloudOS.
199
+
200
+ ╭─ Options ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
201
+ │ * --apikey -k TEXT Your CloudOS API key [required] │
202
+ │ --cloudos-url -c TEXT The CloudOS url you are trying to access to. │
203
+ │ Default=https://cloudos.lifebit.ai. │
204
+ │ * --workspace-id TEXT The specific CloudOS workspace id. [required] │
205
+ │ * --project-name TEXT The name of a CloudOS project. [required] │
206
+ │ * --workflow-name TEXT The name of a CloudOS workflow or pipeline. [required] │
207
+ │ --job-config TEXT A config file similar to a nextflow.config file, but only with the │
208
+ │ parameters to use with your job. │
209
+ │ --parameter -p TEXT A single parameter to pass to the job call. It should be in the following │
210
+ │ form: parameter_name=parameter_value. E.g.: -p │
211
+ │ input=s3://path_to_my_file. You can use this option as many times as │
212
+ │ parameters you want to include. │
213
+ │ --nextflow-profile TEXT A comma separated string indicating the nextflow profile/s to use with │
214
+ │ your job. │
215
+ │ --nextflow-version [22.10.8|24.04.4|22.11.1-edge|latest] Nextflow version to use when executing the workflow in CloudOS. │
216
+ │ Default=22.10.8. │
217
+ │ --git-commit TEXT The git commit hash to run for the selected pipeline. If not specified it │
218
+ │ defaults to the last commit of the default branch. │
219
+ │ --git-tag TEXT The tag to run for the selected pipeline. If not specified it defaults to │
220
+ │ the last commit of the default branch. │
221
+ │ --git-branch TEXT The branch to run for the selected pipeline. If not specified it defaults │
222
+ │ to the last commit of the default branch. │
223
+ │ --job-name TEXT The name of the job. Default=new_job. │
224
+ │ --resumable Whether to make the job able to be resumed or not. │
225
+ │ --do-not-save-logs Avoids process log saving. If you select this option, your job process │
226
+ │ logs will not be stored. │
227
+ │ --job-queue TEXT Name of the job queue to use with a batch job. │
228
+ │ --instance-type TEXT The type of compute instance to use as master node. │
229
+ │ Default=c5.xlarge(aws)|Standard_D4as_v4(azure). │
230
+ │ --instance-disk INTEGER The disk space of the master node instance, in GB. Default=500. │
231
+ │ --storage-mode TEXT Either 'lustre' or 'regular'. Indicates if the user wants to select │
232
+ │ regular or lustre storage. Default=regular. │
233
+ │ --lustre-size INTEGER The lustre storage to be used when --storage-mode=lustre, in GB. It │
234
+ │ should be 1200 or a multiple of it. Default=1200. │
235
+ │ --wait-completion Whether to wait to job completion and report final job status. │
236
+ │ --wait-time INTEGER Max time to wait (in seconds) to job completion. Default=3600. │
237
+ │ --wdl-mainfile TEXT For WDL workflows, which mainFile (.wdl) is configured to use. │
238
+ │ --wdl-importsfile TEXT For WDL workflows, which importsFile (.zip) is configured to use. │
239
+ │ --cromwell-token -t TEXT Specific Cromwell server authentication token. Currently, not necessary │
240
+ │ as apikey can be used instead, but maintained for backwards │
241
+ │ compatibility. │
242
+ │ --repository-platform TEXT Name of the repository platform of the workflow. Default=github. │
243
+ │ --execution-platform [aws|azure|hpc] Name of the execution platform implemented in your CloudOS. Default=aws. │
244
+ │ --hpc-id TEXT ID of your HPC, only applicable when --execution-platform=hpc. │
245
+ │ Default=660fae20f93358ad61e0104b │
246
+ │ --azure-worker-instance-type TEXT The worker node instance type to be used in azure. │
247
+ │ Default=Standard_D4as_v4 │
248
+ │ --azure-worker-instance-disk INTEGER The disk size in GB for the worker node to be used in azure. Default=100 │
249
+ │ --azure-worker-instance-spot Whether the azure worker nodes have to be spot instances or not. │
250
+ │ --cost-limit FLOAT Add a cost limit to your job. Default=30.0 (For no cost limit please use │
251
+ │ -1). │
252
+ │ --accelerate-file-staging Enables AWS S3 mountpoint for quicker file staging. │
253
+ │ --use-private-docker-repository Allows to use private docker repository for running jobs. The Docker user │
254
+ │ account has to be already linked to CloudOS. │
255
+ │ --verbose Whether to print information messages or not. │
256
+ │ --request-interval INTEGER Time interval to request (in seconds) the job status. For large jobs is │
257
+ │ important to use a high number to make fewer requests so that is not │
258
+ │ considered spamming by the API. Default=30. │
259
+ │ --disable-ssl-verification Disable SSL certificate verification. Please, remember that this option │
260
+ │ is not generally recommended for security reasons. │
261
+ │ --ssl-cert TEXT Path to your SSL certificate file. │
262
+ │ --profile TEXT Profile to use from the config file │
263
+ │ --help Show this message and exit. │
264
+ ╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
255
265
  ```
256
266
 
257
267
  #### Send a job to CloudOS
cloudos_cli-2.23.0/cloudos_cli/_version.py DELETED
@@ -1 +0,0 @@
1
- __version__ = '2.23.0'
{cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/LICENSE RENAMED
File without changes
{cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/setup.cfg RENAMED
File without changes
{cloudos_cli-2.23.0 → cloudos_cli-2.24.0}/setup.py RENAMED
File without changes