Usage: bioctl submission [OPTIONS] COMMAND [ARGS]... Commands: submit <workflow_name> 投递工作流 Options: -w, --workspace （*）指定投递的工作流所在Workspace -f, --file （*）Inputs/outputs File Path -m, --datamodel Datamodel 名称 --data-model-rows data-model具体row的id，不输入就是所有id --call-caching 是否callcache，默认为true -d，--description 投递描述 list Options: -w, --workspace （*）指定投递所在Workspace --workflow 指定投递的Workflowm名精确查找 -p, --page 分页页数，默认为1 -s, --size 分页大小，默认为10 --search-word submission name/description中模糊匹配 --status 查询指定状态的投递 --ids 指定submission id展示特定submission完整信息，包括名称、创建时间、挂载目录 query <submission_id> 查询投递状态，不指定run和task时会返回Run列表 Options: -w, --workspace （*）指定投递所在Workspace -r, --run-id string 查询submission下特定run的状态 -t, --task-name string 查询submission下特定task的状态 stop <submission_id> 终止投递如option指定run运行，则只终止单个运行 Options: -w, --workspace （*）指定投递所在Workspace -r, --run-id string 终止特定run-id的运行 delete <submission_id> 删除投递历史 Options: -w, --workspace （*）指定投递所在Workspace log <submission_id> 查看投递日志,不指定run和task时会列出所有run日志的tos地址 Options: -w, --workspace （*）指定投递所在Workspace -r, --run-id string 投递中的具体运行的日志，不指定task时会打印run的日志 -t, --task-name string 投递中的具体运行的task日志，指定时会打印log，output和error日志的内容 output <submission_id> 查看投递所有输出 Options: -w, --workspace （*）指定投递所在Workspace -r, --run-id string 指定投递的具体运行id
bioctl submission submit myworkflow -f workflows/myworkflow/myworkflow.inputs.json -m sample -w demo
以下为输入输出文件的json格式
#input/Output json格式 { "inputs": { "CryoSTARAnalysis.dataset_rel_path": "tutorial_data_1ake/uniform_snr0-0001_ctf", "CryoSTARAnalysis.dataset_zip_file": "s3://bioos-dev-wch4ejbdeig44addonemg/tutorial_data_1ake.zip", "CryoSTARAnalysis.docker_image": "bioos-dev-cn-beijing.cr.volces.com/infcprelease/lab.drug.cryostar_deploy:1.0.0.3", "CryoSTARAnalysis.reconstructAtomic": true, "CryoSTARAnalysis.ref_pdb_rel_path": "tutorial_data_1ake/pdbs/1akeA_50.pdb", "CryoSTARAnalysis.starfile_rel_path": "tutorial_data_1ake/uniform_snr0-0001_ctf/simulation.star", "CryoSTARAnalysis.train_batch_per_gpu": 16, "CryoSTARAnalysis.trainer_device": "NVIDIA-A30", "CryoSTARAnalysis.trainer_devices_num": 2, "CryoSTARAnalysis.trainer_memory": "468G" } }
##终止某个投递 bioctl submission stop <submission_id> -w <workspace_name> ##终止某个工作流运行 bioctl submission stop <submission_id> --run_id <run_id> -w <workspace_name>
bioctl submission query <submission_id> -w <workspace_name>
查询展示如下，每个run对应一个数据实体
+----------+--------------------------+--------------------------------------+------------+ | RunID | StartTime | Status | +----------+--------------------------+--------------------------------------+------------+ | 87546541-f41d-4745-9d1e-4b9b0f27b033 | 2020-10-21T06:34:10.859Z | Running | | cc195aee-41c7-44b0-89e5-4e94ba47f56b | 2020-10-21T05:52:28.360Z | Succeeded | | 7209675e-4277-4d68-8848-725abca6b143 | 2020-10-21T05:52:08.340Z | Succeeded | | 05ed1979-39d4-41db-8535-446919088a2b | 2020-10-21T03:50:01.010Z | Succeeded | | b2394c34-9086-441f-af49-02735b5710ed | 2020-10-21T03:45:40.783Z | Succeeded | +----------+--------------------------+--------------------------------------+------------+
bioctl submission output <submission_id>
输出类似, 如果是字符则显示字符串，如果是文件则提供文件地址
Run rcmnn5sleig4968oearvg: {"CramToBamFlow.outputBai":"s3://bioos-workspaceid/analysis/scmnn5sleig4968oearv0/CramToBamFlow/c2f3e9a6-e640-4809-8d06-9609c774726b/call-CramToBamTask/execution/NA12878.bai","CramToBamFlow.outputBam":"s3://bioos-wcmjk08teig440co6bnr0/analysis/scmnn5sleig4968oearv0/CramToBamFlow/c2f3e9a6-e640-4809-8d06-9609c774726b/call-CramToBamTask/execution/NA12878.bam"} Run rcmnn5sleig4968oeas00: {"CramToBamFlow.outputBai":"s3://bioos-workspaceid/analysis/scmnn5sleig4968oearv0/CramToBamFlow/d705f98c-0523-4325-9233-8c0fca8ce82b/call-CramToBamTask/execution/my_sample_data.bai","CramToBamFlow.outputBam":"s3://bioos-wcmjk08teig440co6bnr0/analysis/scmnn5sleig4968oearv0/CramToBamFlow/d705f98c-0523-4325-9233-8c0fca8ce82b/call-CramToBamTask/execution/my_sample_data.bam"}