Genectl Command
genectl is a command line interface for running commands against KubeGene. You can use genectl to submit your workflow and query the status of workflow execution.
genectl sub
submit genome sequencing workflow to kube-dag controller to execute.
It contains three subcommand:
genectl sub job
genectl sub repjob
genectl sub workflow
Global flags
| Flags | Required | Description |
|---|---|---|
| –kubeconfig string | No | config file used to access kube-apiserver, default “$HOME/.kube/config” |
| –tool-repo string | Yes | directory or URL to tool repository, if it is a URL, it must point to tool file. (default “/root/kubegene/tools”) |
| –dry-run | No | If true, display instantiate execution but do not submit |
genectl sub job
sub job command submits a job which execute a single shell script when perform genome sequencing. You should upload the shell script and sample data to the volume used by this job in preparation stage.
Usage
genectl sub job FILENAME [flags] The args FILENAME is the absolute path of the shell script within the container.
Flags
| Flags | Required | Description |
|---|---|---|
| –cpu string | No | cpu resource required to run this job, default 1 (default “1”) |
| –memory string | No | memory resource required to run this job, default 1G |
| –mount-path string | No | path within the container at which the volume that pvc refer to should be mounted, default the same as the host dir of job script. |
| –pvc string | Yes | the name of pvc that used by the job, the backend storage that the pvc refer to should pre-populate the job script and sample data used by the job. |
| –shell string | No | linux shell used to execute the job script, default sh. |
| –tool string | Yes | tool used by the job, format: toolName:toolVersion |
example
genectl sub job /kubegene/bwa_help.sh --memory 1g --cpu 1 --tool bwa:0.7.12 --pvc pvc-gene
genectl sub repjob
sub repjob command submits a group of job.
Usage
genectl sub repjob FILENAME [flags] The args[0] FILENAME is the absolute path of the shell script within the container. And every line in the shell script is a single job and it follow the format:
bash/sh scriptPath args...
| | |
linux shell abs path within the container shell args
for example:
genectl sub repjob /kubegene/bwa_mem_work.sh --memory 1g --cpu 1 --tool bwa:0.7.12 --pvc pvc-gene
/kubegene/bwa_mem_work.sh is the the absolute path of the shell script within the container.
the content of bwa_mem_work.sh:
sh /kubegene/bwa_mem.sh obs/path/sample1.fastq.gz obs/path/hg19.fa >obs/path/sample1.sam
sh /kubegene/bwa_mem.sh obs/path/sample2.fastq.gz obs/path/hg19.fa >obs/path/sample2.sam
And the script path in your host should keep consistent with the path within the container. You should upload all the shell script and sample data that will be used to the storage volume used by this job.
Flags
| Flags | Required | Description |
|---|---|---|
| –cpu string | No | cpu resource required to run this job, default 1 |
| –memory string | No | memory resource required to run this job, default 1G |
| –mount-path string | No | path within the container at which the volume that pvc refer to should be mounted, default the same as the host dir of job script. |
| –pvc string | Yes | the name of pvc that used by the job, the backend storage that the pvc refer to should pre-populate the job script and sample data used by the job. |
| –shell string | No | linux shell used to execute the job script, default sh (default “sh”) |
| –tool string | Yes | tool used by the job, format: toolName:toolVersion |
example
genectl sub repjob /kubegene/bwa_mem_work.sh --memory 1g --cpu 1 --tool bwa:0.7.12 --pvc pvc-gene
genectl sub workflow
Submit a workflow from a file with specify input json.
Usage
genectl sub workflow FILENAME [flag]
| Flags | Required | Description |
|---|---|---|
| –input string | No | the input json file path. If you do not want to use the input fields defined by the workflow YAML file, you can specify a json file to override this field here. When using a new sample, you can define a new sample name in the json file. |
example
gcs sub workflow wf.yaml --input UserInputs.json
genectl describe
Query the detail execution status of a workflow.
Usage
genectl describe execution executionName [flags]
Flags
| Flags | Required | Description |
|---|---|---|
| –namespace string | No | namespace of execution(default “default”) |
example
genectl describe execution my-exec –n gene-system
genectl get
Query one or a list of execution status of workflows.
Usage
genectl get execution [flags]
Flags
| Flags | Required | Description |
|---|---|---|
| –namespace string | No | namespace of execution(default “default”) |
| –phase strings | No | A comma-separated list for workflow execution phase. Available values: [Running Succeeded Failed Error]. This flag unset means ‘list all phase execution’ |
| –all-namespaces | No | If present, list execution across all namespaces. |
example
List executions in default namespace and in default output format.
genectl get execution
List all executions in default output format.
genectl get execution --all-namespaces
List all executions in yaml output format.
genectl get execution --all-namespaces -o yaml
List executions that are running or succeeded in yaml output format.
genectl get execution --all-namespaces –phase Running,Succeeded
List executions in exec-system namespace that are running or succeeded in yaml output format.
genectl get execution -n exec-system –phase Running,Succeeded
genectl delete
delete an execution of workflow
Usage
genectl delete execution executionName [flags]
Flags
| Flags | Required | Description |
|---|---|---|
| –namespace string | No | namespace of execution(default “default”) |
example
genectl delete execution my-exec –n gene-system