Commands¶

parsec is a set of wrappers for BioBlend’s API. It builds a set of small, useful utilities for talking to Galaxy servers. Each utility is implemented as a subcommand of parsec. This section of the documentation describes these commands.

config
- get_config command
- get_version command
datasets
- download_dataset command
- show_dataset command
datatypes
- get_datatypes command
- get_sniffers command
folders
- create_folder command
- delete_folder command
- get_permissions command
- set_permissions command
- show_folder command
- update_folder command
forms
- create_form command
- get_forms command
- show_form command
ftpfiles
- get_ftp_files command
genomes
- get_genomes command
- install_genome command
- show_genome command
groups
- add_group_role command
- add_group_user command
- create_group command
- delete_group_role command
- delete_group_user command
- get_group_roles command
- get_group_users command
- get_groups command
- show_group command
- update_group command
histories
- create_dataset_collection command
- create_history command
- create_history_tag command
- delete_dataset command
- delete_dataset_collection command
- delete_history command
- download_dataset command
- download_history command
- export_history command
- get_current_history command
- get_histories command
- get_most_recently_used_history command
- get_status command
- show_dataset command
- show_dataset_collection command
- show_dataset_provenance command
- show_history command
- show_matching_datasets command
- undelete_history command
- update_dataset command
- update_dataset_collection command
- update_history command
- upload_dataset_from_library command
jobs
- get_jobs command
- get_state command
- search_jobs command
- show_job command
libraries
- copy_from_dataset command
- create_folder command
- create_library command
- delete_library command
- delete_library_dataset command
- get_folders command
- get_libraries command
- get_library_permissions command
- set_library_permissions command
- show_dataset command
- show_folder command
- show_library command
- upload_file_contents command
- upload_file_from_local_path command
- upload_file_from_server command
- upload_file_from_url command
- upload_from_galaxy_filesystem command
- wait_for_dataset command
quotas
- create_quota command
- delete_quota command
- get_quotas command
- show_quota command
- undelete_quota command
- update_quota command
roles
- create_role command
- get_roles command
- show_role command
tool_data
- delete_data_table command
- get_data_tables command
- reload_data_table command
- show_data_table command
tools
- get_tool_panel command
- get_tools command
- install_dependencies command
- paste_content command
- put_url command
- run_tool command
- show_tool command
- upload_file command
- upload_from_ftp command
toolshed
- get_repositories command
- install_repository_revision command
- show_repository command
toolshed_categories
- get_categories command
- show_category command
toolshed_repositories
- create_repository command
- get_ordered_installable_revisions command
- get_repositories command
toolshed_tools
- search_tools command
users
- create_local_user command
- create_remote_user command
- create_user command
- create_user_apikey command
- delete_user command
- get_current_user command
- get_user_apikey command
- get_users command
- show_user command
utils
- cmp command
- library_recurse command
- wait_on_invocation command
- xunit_xargs command
visual
- get_visualizations command
- show_visualization command
workflows
- cancel_invocation command
- delete_workflow command
- export_workflow_dict command
- export_workflow_json command
- export_workflow_to_local_path command
- get_invocations command
- get_workflow_inputs command
- get_workflows command
- import_shared_workflow command
- import_workflow_dict command
- import_workflow_from_local_path command
- import_workflow_json command
- invoke_workflow command
- run_invocation_step_action command
- run_workflow command
- show_invocation command
- show_invocation_step command
- show_workflow command