cloudos-cli 2.89.1__tar.gz → 2.89.2__tar.gz

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  1. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/PKG-INFO +96 -96
  2. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/README.md +94 -94
  3. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/__main__.py +1 -1
  4. cloudos_cli-2.89.2/cloudos_cli/_version.py +1 -0
  5. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/bash/cli.py +16 -16
  6. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/clos.py +50 -50
  7. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/configure/cli.py +2 -2
  8. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/configure/configure.py +6 -6
  9. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/cromwell/cli.py +14 -14
  10. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/datasets/cli.py +31 -31
  11. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/datasets/datasets.py +27 -27
  12. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/import_wf/__init__.py +1 -1
  13. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/interactive_session/cli.py +44 -44
  14. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/interactive_session/interactive_session.py +22 -22
  15. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/jobs/cli.py +79 -79
  16. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/jobs/job.py +35 -35
  17. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/link/cli.py +8 -8
  18. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/link/link.py +2 -2
  19. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/procurement/cli.py +15 -15
  20. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/procurement/images.py +8 -8
  21. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/projects/cli.py +11 -11
  22. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/queue/cli.py +7 -7
  23. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/queue/queue.py +9 -9
  24. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/utils/array_job.py +5 -5
  25. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/utils/details.py +10 -10
  26. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/utils/nextflow_version.py +3 -3
  27. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/workflows/cli.py +10 -10
  28. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli.egg-info/PKG-INFO +96 -96
  29. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/setup.py +1 -1
  30. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/tests/test_cli_project_create.py +3 -3
  31. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/tests/test_interactive_session/test_create_session.py +3 -3
  32. cloudos_cli-2.89.1/cloudos_cli/_version.py +0 -1
  33. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/LICENSE +0 -0
  34. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/__init__.py +0 -0
  35. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/bash/__init__.py +0 -0
  36. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/configure/__init__.py +0 -0
  37. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/constants.py +0 -0
  38. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/cost/__init__.py +0 -0
  39. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/cost/cost.py +0 -0
  40. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/cromwell/__init__.py +0 -0
  41. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/datasets/__init__.py +0 -0
  42. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/import_wf/import_wf.py +0 -0
  43. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/interactive_session/__init__.py +0 -0
  44. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/jobs/__init__.py +0 -0
  45. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/link/__init__.py +0 -0
  46. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/logging/__init__.py +0 -0
  47. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/logging/logger.py +0 -0
  48. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/procurement/__init__.py +0 -0
  49. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/projects/__init__.py +0 -0
  50. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/queue/__init__.py +0 -0
  51. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/related_analyses/__init__.py +0 -0
  52. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/related_analyses/related_analyses.py +0 -0
  53. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/utils/__init__.py +0 -0
  54. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/utils/cli_helpers.py +0 -0
  55. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/utils/cloud.py +0 -0
  56. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/utils/errors.py +0 -0
  57. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/utils/last_wf.py +0 -0
  58. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/utils/requests.py +0 -0
  59. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/utils/resources.py +0 -0
  60. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli/workflows/__init__.py +0 -0
  61. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli.egg-info/SOURCES.txt +0 -0
  62. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli.egg-info/dependency_links.txt +0 -0
  63. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli.egg-info/entry_points.txt +0 -0
  64. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli.egg-info/requires.txt +0 -0
  65. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/cloudos_cli.egg-info/top_level.txt +0 -0
  66. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/setup.cfg +0 -0
  67. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/tests/__init__.py +0 -0
  68. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/tests/functions_for_pytest.py +0 -0
  69. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/tests/test_cost/__init__.py +0 -0
  70. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/tests/test_cost/test_job_cost.py +0 -0
  71. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/tests/test_details.py +0 -0
  72. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/tests/test_error_messages.py +0 -0
  73. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/tests/test_interactive_session/__init__.py +0 -0
  74. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/tests/test_interactive_session/test_list_sessions.py +0 -0
  75. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/tests/test_logging/__init__.py +0 -0
  76. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/tests/test_logging/test_logger.py +0 -0
  77. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/tests/test_nextflow_version.py +0 -0
  78. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/tests/test_related_analyses/__init__.py +0 -0
  79. {cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/tests/test_related_analyses/test_related_analyses.py +0 -0
{cloudos_cli-2.89.1 → cloudos_cli-2.89.2}/PKG-INFO RENAMED
@@ -1,7 +1,7 @@
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  Metadata-Version: 2.4
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  Name: cloudos_cli
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- Version: 2.89.1
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- Summary: Python package for interacting with CloudOS
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+ Version: 2.89.2
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+ Summary: Python package for interacting with the Lifebit Platform
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  Home-page: https://github.com/lifebit-ai/cloudos-cli
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  Author: David Piñeyro
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  Author-email: david.pineyro@lifebit.ai
@@ -37,7 +37,7 @@ Dynamic: summary
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  [![CI_tests](https://github.com/lifebit-ai/cloudos-cli/actions/workflows/ci.yml/badge.svg)](https://github.com/lifebit-ai/cloudos-cli/actions/workflows/ci.yml)
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- Python package for interacting with CloudOS
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+ Python package for interacting with Lifebit Platform
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  ---
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@@ -203,26 +203,26 @@ To get general information about the tool:
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  cloudos --help
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  ```
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  ```console
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-
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- Usage: cloudos [OPTIONS] COMMAND [ARGS]...
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-
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- CloudOS python package: a package for interacting with CloudOS.
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-
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+
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+ Usage: cloudos [OPTIONS] COMMAND [ARGS]...
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+
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+ CloudOS python package: a package for interacting with Lifebit Platform.
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+
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  ╭─ Options ────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
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  │ --debug Show detailed error information and tracebacks │
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  │ --version Show the version and exit. │
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  │ --help Show this message and exit. │
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  ╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
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  ╭─ Commands ───────────────────────────────────────────────────────────────────────────────────────────────────────────╮
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- │ bash CloudOS bash functionality. │
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- │ configure CloudOS configuration. │
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+ │ bash Lifebit Platform bash functionality. │
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+ │ configure Lifebit Platform configuration. │
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  │ cromwell Cromwell server functionality: check status, start and stop. │
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- │ datasets CloudOS datasets functionality. │
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- │ job CloudOS job functionality: run, check and abort jobs in CloudOS. │
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- │ procurement CloudOS procurement functionality. │
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- │ project CloudOS project functionality: list and create projects in CloudOS. │
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- │ queue CloudOS job queue functionality. │
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- │ workflow CloudOS workflow functionality: list and import workflows. │
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+ │ datasets Lifebit Platform datasets functionality. │
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+ │ job Lifebit Platform job functionality: run, check and abort jobs in Lifebit Platform. │
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+ │ procurement Lifebit Platform procurement functionality. │
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+ │ project Lifebit Platform project functionality: list and create projects in Lifebit Platform. │
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+ │ queue Lifebit Platform job queue functionality. │
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+ │ workflow Lifebit Platform workflow functionality: list and import workflows. │
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  ╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
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  ```
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@@ -233,14 +233,14 @@ cloudos job list --help
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  ```
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  ```console Usage: cloudos job list [OPTIONS]
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- Collect workspace jobs from a CloudOS workspace in CSV or JSON format.
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+ Collect workspace jobs from a Lifebit Platform workspace in CSV or JSON format.
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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. │
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+ │ * --apikey -k TEXT Your Lifebit Platform API key [required] │
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+ │ * --cloudos-url -c TEXT The Lifebit Platform url you are trying to access to. │
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  │ Default=https://cloudos.lifebit.ai. │
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  │ [required] │
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- │ * --workspace-id TEXT The specific CloudOS workspace id. [required] │
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+ │ * --workspace-id TEXT The specific Lifebit Platform workspace id. [required] │
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  │ --output-basename TEXT Output file base name to save jobs list. Default=joblist │
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  │ --output-format [csv|json] The desired file format (file extension) for the output. │
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  │ For json option --all-fields will be automatically set to │
@@ -286,7 +286,7 @@ In the same way, each implemented command has its own subcommands with its own `
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  ## Configuration
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- CloudOS CLI uses a profile-based configuration system to store your credentials and settings securely. This eliminates the need to provide authentication details with every command and allows you to work with multiple CloudOS environments.
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+ CloudOS CLI uses a profile-based configuration system to store your credentials and settings securely. This eliminates the need to provide authentication details with every command and allows you to work with multiple Lifebit Platform environments.
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  Configuration will be saved in the $HOME path folder regardless of operating system. Here, a new folder named `.cloudos` will be created, with files `credentials` and `config` also being created. The structure will look like:
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@@ -320,8 +320,8 @@ cloudos configure --profile {profile-name}
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  The same prompts will appear, including the execution platform (aws or azure). If a profile with the same name already exists, the current parameters will appear in square brackets and can be overwritten or left unchanged by pressing Enter/Return.
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  When configuring a profile, you can specify:
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- - **API Key**: Your CloudOS API credentials
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- - **CloudOS URL**: The CloudOS instance URL
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+ - **API Key**: Your Lifebit Platform API credentials
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+ - **Platform URL**: The Lifebit Platform instance URL
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  - **Project Name**: Default project for commands
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  - **Execution Platform**: `aws` (default) or `azure` - determines default instance types and available features
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  - **Repository Platform**: Version control system (github, gitlab, etc.)
@@ -374,7 +374,7 @@ See [Configuration](#configuration) section above for detailed information on se
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  ### Project
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- Projects in CloudOS provide logical separation of datasets, workflows, and results, making it easier to manage complex research initiatives. You can list all available projects or create new ones using the CLI.
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+ Projects in Lifebit Platform provide logical separation of datasets, workflows, and results, making it easier to manage complex research initiatives. You can list all available projects or create new ones using the CLI.
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  #### List Projects
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@@ -414,7 +414,7 @@ cloudos project list --profile my_profile --output-format json
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  #### Create Projects
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- You can create a new project in your CloudOS workspace using the `project create` command. This command requires the name of the new project and will return the project ID upon successful creation.
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+ You can create a new project in your Lifebit Platform workspace using the `project create` command. This command requires the name of the new project and will return the project ID upon successful creation.
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  ```bash
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  cloudos project create --profile my_profile --new-project "My New Project"
@@ -429,10 +429,10 @@ The expected output is something similar to:
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  ### Queue
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- Job queues are required for running jobs using AWS batch executor. The available job queues in your CloudOS workspace are listed in the "Compute Resources" section in "Settings".
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+ Job queues are required for running jobs using AWS batch executor. The available job queues in your Lifebit Platform workspace are listed in the "Compute Resources" section in "Settings".
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  > [!NOTE]
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- > **Azure Platform**: Queue listing is not available for CloudOS workspaces configured to use Azure execution platform, as Azure does not use AWS batch queues.
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+ > **Azure Platform**: Queue listing is not available for Lifebit Platform workspaces configured to use Azure execution platform, as Azure does not use AWS batch queues.
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  #### List Queues
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@@ -474,11 +474,11 @@ To save queue data to a CSV file:
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  cloudos queue list --profile my_profile --output-format csv
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  ```
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- > NOTE: The queue name that is visible in CloudOS and must be used with the `--job-queue` parameter is the one in the `label` field.
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+ > NOTE: The queue name that is visible in Lifebit Platform and must be used with the `--job-queue` parameter is the one in the `label` field.
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  **Job queues for platform workflows**
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- Platform workflows (those provided by CloudOS in your workspace as modules) run on separate and specific AWS batch queues (system queues). Therefore, CloudOS will automatically assign the valid queue and you should not specify any queue using the `--job-queue` parameter. Any attempt to use this parameter will be ignored. Examples of such platform workflows are "System Tools" and "Data Factory" workflows.
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+ Platform workflows (those provided by Lifebit Platform in your workspace as modules) run on separate and specific AWS batch queues (system queues). Therefore, Lifebit Platform will automatically assign the valid queue and you should not specify any queue using the `--job-queue` parameter. Any attempt to use this parameter will be ignored. Examples of such platform workflows are "System Tools" and "Data Factory" workflows.
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  ### Workflow
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  Workflow list saved to workflow_list.json
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  ```
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- The collected workflows are those that can be found in the "WORKSPACE TOOLS" section in CloudOS.
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+ The collected workflows are those that can be found in the "WORKSPACE TOOLS" section in Lifebit Platform.
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  #### Import a Nextflow Workflow
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- You can import new workflows to your CloudOS workspaces. The requirements are:
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+ You can import new workflows to your Lifebit Platform workspaces. The requirements are:
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  - The workflow must be a Nextflow pipeline
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  - The workflow repository must be located at GitHub, GitLab or BitBucket Server (specified by the `--repository-platform` option. Available options: `github`, `gitlab` and `bitbucketServer`)
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- - If your repository is private, you must have access to the repository and have linked your GitHub, Gitlab or Bitbucket server accounts to CloudOS
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+ - If your repository is private, you must have access to the repository and have linked your GitHub, Gitlab or Bitbucket server accounts to Lifebit Platform
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  **Usage of the workflow import command**
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- To import GitHub workflows to CloudOS:
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+ To import GitHub workflows to Lifebit Platform:
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  ```bash
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  # Example workflow to import: https://github.com/lifebit-ai/DeepVariant
@@ -547,7 +547,7 @@ cloudos workflow import --profile my_profile --workflow-url "https://github.com/
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  The expected output will be:
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  ```console
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- CloudOS workflow functionality: list and import workflows.
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+ Lifebit Platform workflow functionality: list and import workflows.
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  Executing workflow import...
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@@ -562,16 +562,16 @@ Optionally, you can add a link to your workflow documentation by providing the U
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  cloudos workflow import --profile my_profile --workflow-url "https://github.com/lifebit-ai/DeepVariant" --workflow-name "new_name_for_the_github_workflow" --workflow-docs-link "https://github.com/lifebit-ai/DeepVariant/blob/master/README.md" --repository-platform github
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  ```
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- > NOTE: Importing workflows using cloudos-cli is not yet available in all CloudOS workspaces. If you try to use this feature in a non-prepared workspace you will get the following error message: `It seems your API key is not authorised. Please check if your workspace has support for importing workflows using cloudos-cli`.
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+ > NOTE: Importing workflows using cloudos-cli is not yet available in all Lifebit Platform workspaces. If you try to use this feature in a non-prepared workspace you will get the following error message: `It seems your API key is not authorised. Please check if your workspace has support for importing workflows using cloudos-cli`.
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  ### Nextflow Jobs
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- The job commands allow you to submit, monitor, and manage computational workflows on CloudOS. This includes both Nextflow pipelines and bash scripts, with support for various execution platforms.
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+ The job commands allow you to submit, monitor, and manage computational workflows on Lifebit Platform. This includes both Nextflow pipelines and bash scripts, with support for various execution platforms.
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  #### Submit a Job
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- You can submit Nextflow workflows to CloudOS using either configuration files or command-line parameters. Jobs can be configured with specific compute resources, execution platforms, parameters, etc.
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+ You can submit Nextflow workflows to Lifebit Platform using either configuration files or command-line parameters. Jobs can be configured with specific compute resources, execution platforms, parameters, etc.
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  First, configure your local environment to ease parameter input. We will try to submit a small toy example already available:
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@@ -651,7 +651,7 @@ If everything went well, you should see something like:
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  ```console
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  Executing run...
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- Job successfully launched to CloudOS, please check the following link: https://cloudos.lifebit.ai/app/advanced-analytics/analyses/62c83a1191fe06013b7ef355
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+ Job successfully launched to Lifebit Platform, please check the following link: https://cloudos.lifebit.ai/app/advanced-analytics/analyses/62c83a1191fe06013b7ef355
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  Your assigned job id is: 62c83a1191fe06013b7ef355
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  Your current job status is: initializing
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  To further check your job status you can either go to https://cloudos.lifebit.ai/app/advanced-analytics/analyses/62c83a1191fe06013b7ef355 or use the following command:
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  ```console
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  Executing run...
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- Job successfully launched to CloudOS, please check the following link: https://cloudos.lifebit.ai/app/advanced-analytics/analyses/62c83a6191fe06013b7ef363
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+ Job successfully launched to Lifebit Platform, please check the following link: https://cloudos.lifebit.ai/app/advanced-analytics/analyses/62c83a6191fe06013b7ef363
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  Your assigned job id is: 62c83a6191fe06013b7ef363
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  Please, wait until job completion or max wait time of 3600 seconds is reached.
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  Your current job status is: initializing.
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  **AWS Executor Support**
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- CloudOS supports [AWS batch](https://www.nextflow.io/docs/latest/executor.html?highlight=executors#aws-batch) executor by default.
715
+ Lifebit Platform supports [AWS batch](https://www.nextflow.io/docs/latest/executor.html?highlight=executors#aws-batch) executor by default.
716
716
  You can specify the AWS batch queue to use from the ones available in your workspace (see [here](#list-job-queues)) by specifying its name with the `--job-queue` parameter. If none is specified, the most recent suitable queue in your workspace will be selected by default.
717
717
 
718
718
  Example command:
@@ -721,13 +721,13 @@ Example command:
721
721
  cloudos job run --profile my_profile --workflow-name rnatoy --job-config cloudos_cli/examples/rnatoy.config --resumable
722
722
  ```
723
723
 
724
- > Note: From cloudos-cli 2.7.0, the default executor is AWS batch. The previous Apache [ignite](https://www.nextflow.io/docs/latest/ignite.html#apache-ignite) executor is being removed progressively from CloudOS, so most likely will not be available in your CloudOS. Cloudos-cli still supports ignite during this period by adding the `--ignite` flag to the `cloudos job run` command. Please note that if you use the `--ignite` flag in a CloudOS without ignite support, the command will fail.
724
+ > Note: From cloudos-cli 2.7.0, the default executor is AWS batch. The previous Apache [ignite](https://www.nextflow.io/docs/latest/ignite.html#apache-ignite) executor is being removed progressively from Lifebit Platform, so most likely will not be available in your Lifebit Platform. Cloudos-cli still supports ignite during this period by adding the `--ignite` flag to the `cloudos job run` command. Please note that if you use the `--ignite` flag in a Lifebit Platform without ignite support, the command will fail.
725
725
 
726
726
  **Azure Execution Platform Support**
727
727
 
728
- CloudOS can also be configured to use Microsoft Azure compute platforms. If your CloudOS is configured to use Azure, you will need to take into consideration the following:
728
+ Lifebit Platform can also be configured to use Microsoft Azure compute platforms. If your Lifebit Platform is configured to use Azure, you will need to take into consideration the following:
729
729
 
730
- - When sending jobs to CloudOS using `cloudos job run` command, please use the option `--execution-platform azure`
730
+ - When sending jobs to Lifebit Platform using `cloudos job run` command, please use the option `--execution-platform azure`
731
731
  - Azure only supports Nextflow version `22.11.1-edge`. If you specify a different version, CloudOS CLI will display a warning and automatically use `22.11.1-edge` instead
732
732
  - Due to the lack of AWS batch queues in Azure, `cloudos queue list` command is not working
733
733
 
@@ -739,7 +739,7 @@ cloudos job run --profile my_profile --workflow-name rnatoy --job-config cloudos
739
739
 
740
740
  **HPC Execution Support**
741
741
 
742
- CloudOS is also prepared to use an HPC compute infrastructure. For such cases, you will need to take into account the following for your job submissions using `cloudos job run` command:
742
+ Lifebit Platform is also prepared to use an HPC compute infrastructure. For such cases, you will need to take into account the following for your job submissions using `cloudos job run` command:
743
743
 
744
744
  - Use the following parameter: `--execution-platform hpc`
745
745
  - Indicate the HPC ID using: `--hpc-id XXXX`
@@ -825,7 +825,7 @@ Jobs are displayed with colored visual status indicators:
825
825
 
826
826
  **Clickable Job IDs**
827
827
 
828
- Job IDs in the table are clickable hyperlinks (when supported by your terminal) that open the job details page in CloudOS.
828
+ Job IDs in the table are clickable hyperlinks (when supported by your terminal) that open the job details page in Lifebit Platform.
829
829
 
830
830
  **Job Listing Control Options**
831
831
 
@@ -966,7 +966,7 @@ cloudos job list --profile my_profile --last-n-jobs all --filter-workflow rnatoy
966
966
 
967
967
  #### Get Job Results
968
968
 
969
- The following command allows you to get the path where CloudOS stores the output files for a job. This can be used only on your user's jobs and for jobs with "completed" status.
969
+ The following command allows you to get the path where Lifebit Platform stores the output files for a job. This can be used only on your user's jobs and for jobs with "completed" status.
970
970
 
971
971
  Example:
972
972
  ```bash
@@ -1098,7 +1098,7 @@ cloudos job resume \
1098
1098
 
1099
1099
  #### Abort Jobs
1100
1100
 
1101
- Aborts jobs in the CloudOS workspace that are either running or initializing. It can be used with one or more job IDs provided as a comma-separated string using the `--job-ids` parameter.
1101
+ Aborts jobs in the Lifebit Platform workspace that are either running or initializing. It can be used with one or more job IDs provided as a comma-separated string using the `--job-ids` parameter.
1102
1102
 
1103
1103
  ##### Basic Usage
1104
1104
 
@@ -1127,9 +1127,9 @@ Job 680a3cf80e56949775c02f16 aborted successfully.
1127
1127
 
1128
1128
  ##### Additional Options
1129
1129
 
1130
- - `--workspace-id`: The CloudOS workspace ID (can be set in profile)
1131
- - `--apikey`: Your CloudOS API key (can be set in profile)
1132
- - `--cloudos-url`: The CloudOS URL (default: https://cloudos.lifebit.ai)
1130
+ - `--workspace-id`: The Lifebit Platform workspace ID (can be set in profile)
1131
+ - `--apikey`: Your Lifebit Platform API key (can be set in profile)
1132
+ - `--cloudos-url`: The Lifebit Platform URL (default: https://cloudos.lifebit.ai)
1133
1133
  - `--verbose`: Print detailed information messages
1134
1134
  - `--disable-ssl-verification`: Disable SSL certificate verification (not recommended)
1135
1135
  - `--ssl-cert`: Path to your SSL certificate file
@@ -1208,7 +1208,7 @@ This file can later be used when running a job with `cloudos job run --job-confi
1208
1208
 
1209
1209
  #### Get Job Workdir
1210
1210
 
1211
- To get the working directory of a job submitted to CloudOS:
1211
+ To get the working directory of a job submitted to Lifebit Platform:
1212
1212
 
1213
1213
  ```shell
1214
1214
  cloudos job workdir \
@@ -1219,7 +1219,7 @@ cloudos job workdir \
1219
1219
  The output should be something similar to:
1220
1220
 
1221
1221
  ```console
1222
- CloudOS job functionality: run, check and abort jobs in CloudOS.
1222
+ Lifebit Platform job functionality: run, check and abort jobs in Lifebit Platform.
1223
1223
 
1224
1224
  Finding working directory path...
1225
1225
  Working directory for job 68747bac9e7fe38ec6e022ad: az://123456789000.blob.core.windows.net/cloudos-987652349087/projects/455654676/jobs/54678856765/work
@@ -1297,9 +1297,9 @@ cloudos job logs --profile my_profile --job-id "12345678910" --link --session-id
1297
1297
 
1298
1298
  #### Get Job Costs
1299
1299
 
1300
- You can retrieve detailed cost information for any job in your CloudOS workspace using the `job cost` command. This provides insights into compute costs, storage usage, and runtime metrics to help optimize workflows and manage expenses.
1300
+ You can retrieve detailed cost information for any job in your Lifebit Platform workspace using the `job cost` command. This provides insights into compute costs, storage usage, and runtime metrics to help optimize workflows and manage expenses.
1301
1301
 
1302
- The cost information is retrieved from CloudOS and can be displayed in multiple formats:
1302
+ The cost information is retrieved from Lifebit Platform and can be displayed in multiple formats:
1303
1303
 
1304
1304
  - **Console display**: Rich formatted tables with pagination for easy viewing
1305
1305
  - **CSV**: Structured data for analysis and reporting
@@ -1444,9 +1444,9 @@ cat 62c83a1191fe06013b7ef355_costs.json
1444
1444
 
1445
1445
  #### Get Job Related Analyses
1446
1446
 
1447
- You can view related jobs that share the same working directory in a CloudOS workspace by using the `job related` command. This feature helps track job lineages, resume workflows, and understand job relationships.
1447
+ You can view related jobs that share the same working directory in a Lifebit Platform workspace by using the `job related` command. This feature helps track job lineages, resume workflows, and understand job relationships.
1448
1448
 
1449
- The information is retrieved from CloudOS and can be displayed in multiple formats:
1449
+ The information is retrieved from Lifebit Platform and can be displayed in multiple formats:
1450
1450
 
1451
1451
  - **Console display**: Rich formatted tables with pagination
1452
1452
  - **JSON**: Complete job data for programmatic processing
@@ -1484,7 +1484,7 @@ The table displays key information for each related job:
1484
1484
  - **Status**: Current job state (initializing, running, completed, aborting, aborted, failed)
1485
1485
  - **Name**: Job name assigned when submitted
1486
1486
  - **Owner**: User who submitted the job (first name and last name)
1487
- - **ID**: Job identifier in CloudOS
1487
+ - **ID**: Job identifier in Lifebit Platform
1488
1488
  - **Submit time**: When the job was submitted (formatted as YYYY-MM-DD HH:MM:SS)
1489
1489
  - **Run time**: Actual execution time (formatted as hours, minutes, seconds)
1490
1490
  - **Total Cost**: Compute cost in USD
@@ -1552,7 +1552,7 @@ Related analyses are particularly useful for:
1552
1552
 
1553
1553
  #### Delete Job Results
1554
1554
 
1555
- CloudOS allows you to permanently delete job results directories to manage storage and clean up completed analyses. This feature provides a safe way to remove final analysis results with built-in confirmation prompts and status tracking.
1555
+ Lifebit Platform allows you to permanently delete job results directories to manage storage and clean up completed analyses. This feature provides a safe way to remove final analysis results with built-in confirmation prompts and status tracking.
1556
1556
 
1557
1557
  > [!WARNING]
1558
1558
  > Deleting job results is **irreversible**. All data and backups will be permanently removed and cannot be recovered. Use this feature with caution.
@@ -1628,7 +1628,7 @@ For bulk deletion of job results and working directories across multiple jobs in
1628
1628
 
1629
1629
  #### Archive Jobs
1630
1630
 
1631
- CloudOS allows you to archive completed jobs to organize and manage your analysis history.
1631
+ Lifebit Platform allows you to archive completed jobs to organize and manage your analysis history.
1632
1632
 
1633
1633
  > [!NOTE]
1634
1634
  > Archiving jobs does not delete any data or results. It simply adds metadata to mark jobs as archived for organizational purposes.
@@ -1713,14 +1713,14 @@ Job 'valid_job' archived successfully.
1713
1713
  - `--verbose`: Display detailed information about the archiving process
1714
1714
  - `--profile`: Use a specific configuration profile
1715
1715
  - `--workspace-id`: Specify the workspace ID (if not using profiles)
1716
- - `--apikey`: Your CloudOS API key (if not using profiles)
1716
+ - `--apikey`: Your Lifebit Platform API key (if not using profiles)
1717
1717
 
1718
1718
  > [!TIP]
1719
1719
  > Use the `cloudos job list` command to identify jobs you want to archive. You can filter by status, project, or other criteria to find specific jobs for archiving.
1720
1720
 
1721
1721
  #### Unarchive Jobs
1722
1722
 
1723
- CloudOS allows you to restore archived jobs back to their active state. Unarchiving removes the archived status while preserving all job data, results, and history.
1723
+ Lifebit Platform allows you to restore archived jobs back to their active state. Unarchiving removes the archived status while preserving all job data, results, and history.
1724
1724
 
1725
1725
  > [!NOTE]
1726
1726
  > Unarchiving jobs does not modify any data or results. It simply removes the archived metadata flag, making jobs appear as regular (non-archived) jobs again.
@@ -1805,7 +1805,7 @@ Job 'valid_job' unarchived successfully.
1805
1805
  - `--verbose`: Display detailed information about the unarchiving process
1806
1806
  - `--profile`: Use a specific configuration profile
1807
1807
  - `--workspace-id`: Specify the workspace ID (if not using profiles)
1808
- - `--apikey`: Your CloudOS API key (if not using profiles)
1808
+ - `--apikey`: Your Lifebit Platform API key (if not using profiles)
1809
1809
 
1810
1810
  **Managing Job Lifecycle**
1811
1811
 
@@ -1819,12 +1819,12 @@ Use the archive and unarchive commands together to manage your job organization:
1819
1819
  > Archived jobs remain fully accessible - archiving is purely for organizational purposes. Use `cloudos job list` with appropriate filters to view and manage both archived and active jobs.
1820
1820
 
1821
1821
  ### Bash Jobs
1822
- Execute bash scripts on CloudOS for custom processing workflows. Bash jobs allow you to run shell commands with custom parameters and are ideal for data preprocessing or simple computational tasks.
1822
+ Execute bash scripts on Lifebit Platform for custom processing workflows. Bash jobs allow you to run shell commands with custom parameters and are ideal for data preprocessing or simple computational tasks.
1823
1823
 
1824
1824
  #### Send Array Job
1825
1825
 
1826
1826
 
1827
- A bash job can be sent to CloudOS using the command `bash` and the subcommand `job`. In this case, the `--workflow-name` must be a bash job already present in the platform. Bash jobs are identified by bash icon (unlike Nextflow jobs, which are identified with Nextflow icon).
1827
+ A bash job can be sent to Lifebit Platform using the command `bash` and the subcommand `job`. In this case, the `--workflow-name` must be a bash job already present in the platform. Bash jobs are identified by bash icon (unlike Nextflow jobs, which are identified with Nextflow icon).
1828
1828
 
1829
1829
  ```bash
1830
1830
  cloudos bash job \
@@ -1848,9 +1848,9 @@ Each `--parameter` can have a different prefix, either '--', '-', or '', dependi
1848
1848
  If everything went well, you should see something like:
1849
1849
 
1850
1850
  ```console
1851
- CloudOS bash functionality.
1851
+ Lifebit Platform bash functionality.
1852
1852
 
1853
- Job successfully launched to CloudOS, please check the following link: https://cloudos.lifebit.ai/app/advanced-analytics/analyses/682622d09f305de717327334
1853
+ Job successfully launched to Lifebit Platform, please check the following link: https://cloudos.lifebit.ai/app/advanced-analytics/analyses/682622d09f305de717327334
1854
1854
  Your assigned job id is: 682622d09f305de717327334
1855
1855
 
1856
1856
  Your current job status is: initializing
@@ -2182,8 +2182,8 @@ cloudos interactive-session create \
2182
2182
  - `--shutdown-in`: Auto-shutdown duration (e.g., `8h`, `2d`, `30m`, default: `12h`)
2183
2183
 
2184
2184
  **Data & Storage Management:**
2185
- - `--mount`: Mount a data file into the session. Supports both CloudOS datasets and S3 files (AWS only). Format: `project_name/dataset_path` (e.g., `leila-test/Data/file.csv`) or `s3://bucket/path/to/file` (e.g., `s3://my-bucket/data/file.csv`). Can be used multiple times.
2186
- - `--link`: Link a folder into the session for read/write access (AWS only). Supports S3 folders and CloudOS folders. Format: `s3://bucket/prefix` (e.g., `s3://my-bucket/data/`) or `project_name/folder_path` (e.g., `leila-test/AnalysesResults/analysis_id/results`). Can be used multiple times. **Note:** Linking is not supported on Azure. Use CloudOS file explorer for data access.
2185
+ - `--mount`: Mount a data file into the session. Supports both Lifebit Platform datasets and S3 files (AWS only). Format: `project_name/dataset_path` (e.g., `leila-test/Data/file.csv`) or `s3://bucket/path/to/file` (e.g., `s3://my-bucket/data/file.csv`). Can be used multiple times.
2186
+ - `--link`: Link a folder into the session for read/write access (AWS only). Supports S3 folders and Lifebit Platform folders. Format: `s3://bucket/prefix` (e.g., `s3://my-bucket/data/`) or `project_name/folder_path` (e.g., `leila-test/AnalysesResults/analysis_id/results`). Can be used multiple times. **Note:** Linking is not supported on Azure. Use Lifebit Platform file explorer for data access.
2187
2187
 
2188
2188
  **Backend-Specific:**
2189
2189
  - `--r-version`: R version for RStudio (options: `4.4.2`, `4.5.2`) - **optional for rstudio** (default: `4.4.2`)
@@ -2533,7 +2533,7 @@ The command automatically loads from profile (via `@with_profile_config` decorat
2533
2533
 
2534
2534
  **Optional Overrides from Profile:**
2535
2535
  - `--apikey` (optional): Override API key from profile
2536
- - `--cloudos-url` (optional): Override CloudOS URL from profile
2536
+ - `--cloudos-url` (optional): Override Lifebit Platform URL from profile
2537
2537
  - `--workspace-id` (optional): Override workspace ID from profile
2538
2538
 
2539
2539
  **Optional Behavior Flags:**
@@ -2606,11 +2606,11 @@ All configuration parameters are optional. If not specified, the session resumes
2606
2606
 
2607
2607
  ### Datasets
2608
2608
 
2609
- Manage files and folders within your CloudOS File Explorer programmatically. These commands provide comprehensive file management capabilities for organizing research data and results.
2609
+ Manage files and folders within your Lifebit Platform File Explorer programmatically. These commands provide comprehensive file management capabilities for organizing research data and results.
2610
2610
 
2611
2611
  #### List Files
2612
2612
 
2613
- Browse files and folders within your CloudOS projects. Use the `--details` flag to get comprehensive information about file ownership, sizes, and modification dates.
2613
+ Browse files and folders within your Lifebit Platform projects. Use the `--details` flag to get comprehensive information about file ownership, sizes, and modification dates.
2614
2614
 
2615
2615
  ```bash
2616
2616
  cloudos datasets ls <path> --profile <profile>
@@ -2770,7 +2770,7 @@ cloudos datasets mkdir <new_folder_path> --profile my_profile
2770
2770
 
2771
2771
  #### Remove Files or Folders
2772
2772
 
2773
- Remove unnecessary files or empty folders from your File Explorer. Note that this removes files from CloudOS but not from underlying cloud storage.
2773
+ Remove unnecessary files or empty folders from your File Explorer. Note that this removes files from Lifebit Platform but not from underlying cloud storage.
2774
2774
 
2775
2775
  > [!NOTE]
2776
2776
  > Files and folders can be removed in the `Data` datasets and its subfolders.
@@ -2819,12 +2819,12 @@ cloudos link "Data/MyFolder" --project-name my-project --session-id <SESSION_ID>
2819
2819
  **Command options:**
2820
2820
 
2821
2821
  - `PATH`: S3 path to link (positional argument, required if `--job-id` is not provided)
2822
- - `--apikey` / `-k`: Your CloudOS API key (required)
2823
- - `--cloudos-url` / `-c`: The CloudOS URL (default: https://cloudos.lifebit.ai)
2824
- - `--workspace-id`: The specific CloudOS workspace ID (required)
2825
- - `--session-id`: The specific CloudOS interactive session ID (required)
2826
- - `--job-id`: The job ID in CloudOS (links results, workdir, and logs by default)
2827
- - `--project-name`: CloudOS project name (required for File Explorer paths)
2822
+ - `--apikey` / `-k`: Your Lifebit Platform API key (required)
2823
+ - `--cloudos-url` / `-c`: The Lifebit Platform URL (default: https://cloudos.lifebit.ai)
2824
+ - `--workspace-id`: The specific Lifebit Platform workspace ID (required)
2825
+ - `--session-id`: The specific Lifebit Platform interactive session ID (required)
2826
+ - `--job-id`: The job ID in Lifebit Platform (links results, workdir, and logs by default)
2827
+ - `--project-name`: Lifebit Platform project name (required for File Explorer paths)
2828
2828
  - `--results`: Link only results folder (only works with `--job-id`)
2829
2829
  - `--workdir`: Link only working directory (only works with `--job-id`)
2830
2830
  - `--logs`: Link only logs folder (only works with `--job-id`)
@@ -2868,7 +2868,7 @@ The command provides clear error messages for common scenarios:
2868
2868
 
2869
2869
  ### Procurement
2870
2870
 
2871
- CloudOS supports procurement functionality to manage and list images associated with organizations within a given procurement. This feature is useful for administrators and users who need to view available container images across different organizations in their procurement.
2871
+ Lifebit Platform supports procurement functionality to manage and list images associated with organizations within a given procurement. This feature is useful for administrators and users who need to view available container images across different organizations in their procurement.
2872
2872
 
2873
2873
  #### List Procurement Images
2874
2874
 
@@ -2884,9 +2884,9 @@ cloudos procurement images ls \
2884
2884
 
2885
2885
  **Command options:**
2886
2886
 
2887
- - `--apikey` / `-k`: Your CloudOS API key (required)
2888
- - `--cloudos-url` / `-c`: The CloudOS URL you are trying to access (default: https://cloudos.lifebit.ai)
2889
- - `--procurement-id`: The specific CloudOS procurement ID (required)
2887
+ - `--apikey` / `-k`: Your Lifebit Platform API key (required)
2888
+ - `--cloudos-url` / `-c`: The Lifebit Platform URL you are trying to access (default: https://cloudos.lifebit.ai)
2889
+ - `--procurement-id`: The specific Lifebit Platform procurement ID (required)
2890
2890
  - `--page`: The response page number (default: 1)
2891
2891
  - `--limit`: The page size limit (default: 10)
2892
2892
  - `--disable-ssl-verification`: Disable SSL certificate verification
@@ -2920,7 +2920,7 @@ This is particularly useful for understanding what container images are availabl
2920
2920
 
2921
2921
  #### Set Procurement Organization Image
2922
2922
 
2923
- You can set a custom image ID or name for an organization within a procurement using the `cloudos procurement images set` command. This allows you to override the default CloudOS images with your own custom images for specific organizations.
2923
+ You can set a custom image ID or name for an organization within a procurement using the `cloudos procurement images set` command. This allows you to override the default Lifebit Platform images with your own custom images for specific organizations.
2924
2924
 
2925
2925
  To set a custom image for an organization, use the following command:
2926
2926
 
@@ -2930,11 +2930,11 @@ cloudos procurement images set --profile procurement_profile --image-type "JobDe
2930
2930
 
2931
2931
  **Set command options:**
2932
2932
 
2933
- - `--apikey` / `-k`: Your CloudOS API key (required)
2934
- - `--cloudos-url` / `-c`: The CloudOS URL you are trying to access (default: https://cloudos.lifebit.ai)
2935
- - `--procurement-id`: The specific CloudOS procurement ID (required)
2933
+ - `--apikey` / `-k`: Your Lifebit Platform API key (required)
2934
+ - `--cloudos-url` / `-c`: The Lifebit Platform URL you are trying to access (default: https://cloudos.lifebit.ai)
2935
+ - `--procurement-id`: The specific Lifebit Platform procurement ID (required)
2936
2936
  - `--organisation-id`: The organization ID where the change will be applied (required)
2937
- - `--image-type`: The CloudOS resource image type (required). Possible values:
2937
+ - `--image-type`: The Lifebit Platform resource image type (required). Possible values:
2938
2938
  - `RegularInteractiveSessions`
2939
2939
  - `SparkInteractiveSessions`
2940
2940
  - `RStudioInteractiveSessions`
@@ -2959,7 +2959,7 @@ cloudos procurement images set --profile procurement_profile --image-type "JobDe
2959
2959
 
2960
2960
  #### Reset Procurement Organization Image
2961
2961
 
2962
- You can reset an organization's image configuration back to CloudOS defaults using the `cloudos procurement images reset` command. This removes any custom image configurations and restores the original CloudOS defaults.
2962
+ You can reset an organization's image configuration back to Lifebit Platform defaults using the `cloudos procurement images reset` command. This removes any custom image configurations and restores the original Lifebit Platform defaults.
2963
2963
 
2964
2964
  To reset an organization's image to defaults, use the following command:
2965
2965
 
@@ -2969,11 +2969,11 @@ cloudos procurement images reset --profile procurement_profile --image-type "Job
2969
2969
 
2970
2970
  **Reset command options:**
2971
2971
 
2972
- - `--apikey` / `-k`: Your CloudOS API key (required)
2973
- - `--cloudos-url` / `-c`: The CloudOS URL you are trying to access (default: https://cloudos.lifebit.ai)
2974
- - `--procurement-id`: The specific CloudOS procurement ID (required)
2972
+ - `--apikey` / `-k`: Your Lifebit Platform API key (required)
2973
+ - `--cloudos-url` / `-c`: The Lifebit Platform URL you are trying to access (default: https://cloudos.lifebit.ai)
2974
+ - `--procurement-id`: The specific Lifebit Platform procurement ID (required)
2975
2975
  - `--organisation-id`: The organization ID where the change will be applied (required)
2976
- - `--image-type`: The CloudOS resource image type (required). Same values as for `set` command
2976
+ - `--image-type`: The Lifebit Platform resource image type (required). Same values as for `set` command
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  - `--provider`: The cloud provider (required). Currently only `aws` is supported
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  - `--region`: The cloud region (required). Currently only AWS regions are supported
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  - `--disable-ssl-verification`: Disable SSL certificate verification
@@ -2983,7 +2983,7 @@ cloudos procurement images reset --profile procurement_profile --image-type "Job
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  **Reset command example:**
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2985
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  ```bash
2986
- # Reset image configuration to CloudOS defaults
2986
+ # Reset image configuration to Lifebit Platform defaults
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2987
  cloudos procurement images reset --profile procurement_profile --image-type "JobDefault" --provider "aws" --region "us-east-1" --procurement-id "your_procurement_id_here" --organisation-id "your_organization_id"
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  ```
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@@ -2992,7 +2992,7 @@ cloudos procurement images reset --profile procurement_profile --image-type "Job
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  #### Manage Cromwell Server
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2995
- In order to run WDL pipelines, a Cromwell server in CloudOS should be running. This server can be accessed to check its status, restart it or stop it, using the following commands:
2995
+ In order to run WDL pipelines, a Cromwell server in Lifebit Platform should be running. This server can be accessed to check its status, restart it or stop it, using the following commands:
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  ```bash
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  # Check Cromwell status
@@ -3030,7 +3030,7 @@ Stopping Cromwell server...
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  To run WDL workflows, `cloudos job run` command can be used normally, but adding two extra parameters:
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- - `--wdl-mainfile`: name of the mainFile (*.wdl) file used by the CloudOS workflow.
3033
+ - `--wdl-mainfile`: name of the mainFile (*.wdl) file used by the Lifebit Platform workflow.
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  - `--wdl-importsfile` [Optional]: name of the workflow imported file (importsFile, *.zip).
3035
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3036
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  All the rest of the `cloudos job run` functionality is available.
@@ -3079,7 +3079,7 @@ Executing run...
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  --workspace-id $WORKSPACE_ID
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  *******************************************************************************
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3082
- Job successfully launched to CloudOS, please check the following link: ****
3082
+ Job successfully launched to Lifebit Platform, please check the following link: ****
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  Your assigned job id is: ****
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  Please, wait until job completion or max wait time of 3600 seconds is reached.
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  Your current job status is: initializing.