table(table table-bordered table-condensed).
|Environment variable|Description|
-|@JOB_UUID@|UUID of the current "Job":schema/Job.html|
-|@TASK_UUID@|UUID of the current "JobTask":schema/JobTask.html|
+|@JOB_UUID@|UUID of the current "Job":methods/jobs.html|
+|@TASK_UUID@|UUID of the current "JobTask":methods/job_tasks.html|
|@ARVADOS_API_HOST@|Hostname and port number of API server|
|@ARVADOS_API_TOKEN@|Authentication token to use with API calls made by the current task|
$sys.stderr.write("current task sequence number is %d"
% task['sequence'])
</pre>
-
h2. Job API (deprecated)
-# To submit work, create a "job":{{site.baseurl}}/api/methods/job.html . If the same job has been submitted in the past, it will return an existing job in @Completed@ state.
+# To submit work, create a "job":{{site.baseurl}}/api/methods/jobs.html . If the same job has been submitted in the past, it will return an existing job in @Completed@ state.
# The dispatcher process will notice a new job in @Queued@ state and attempt to allocate nodes to run the job.
# The job executes.
# Retrieve the @output@ field with the portable data hash of the collection with the output files of the job.
When a job is submitted to the queue using the **create** method, the @script_version@ attribute is updated to a full 40-character Git commit hash based on the current content of the specified repository. If @script_version@ cannot be resolved, the job submission is rejected.
-fn1. See the "note about specifying Git commits on the Job resource page":{{site.baseurl}}/api/schema/Job.html#script_version for more detail.
+fn1. See the "note about specifying Git commits":#script_version for more detail.
h4. Specialized filters
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
-|pipeline_template_uuid|string|The "pipeline template":pipeline_template.html that this instance was created from.||
+|pipeline_template_uuid|string|The "pipeline template":pipeline_templates.html that this instance was created from.||
|name|string|||
|components|hash|||
|success|boolean|||
title: Subscribing to events
...
-Arvados applications can subscribe to a live event stream from the database. Events are described in the "Log record schema.":{{site.baseurl}}/api/schema/Log.html
+Arvados applications can subscribe to a live event stream from the database. Events are described in the "Log resource.":{{site.baseurl}}/api/methods/logs.html
<notextile>
{% code 'events_py' as python %}
title: "Pipeline template reference"
...
-Pipeline template options are described on the "pipeline template schema page.":{{site.baseurl}}/api/schema/PipelineTemplate.html
+Pipeline template options are described on the "pipeline template schema page.":{{site.baseurl}}/api/methods/pipeline_templates.html
* @"name"@ is a human-readable name for the pipeline.
* @"components"@ is a set of scripts or commands that make up the pipeline. Each component is given an identifier (@"bwa-mem"@ and @"SortSam"@) in this example).
-** Each entry in components @"components"@ is an Arvados job submission. For more information about individual jobs, see the "job object reference":{{site.baseurl}}/api/schema/Job.html and "job create method.":{{site.baseurl}}/api/methods/jobs.html#create
+** Each entry in components @"components"@ is an Arvados job submission. For more information about individual jobs, see the "job resource reference.":{{site.baseurl}}/api/methods/jobs.html
* @"repository"@, @"script_version"@, and @"script"@ indicate that we intend to use the external @"run-command"@ tool wrapper that is part of the Arvados. These parameters are described in more detail in "Writing a script":tutorial-firstscript.html.
* @"runtime_constraints"@ describes runtime resource requirements for the component.
** @"docker_image"@ specifies the "Docker":https://www.docker.com/ runtime environment in which to run the job. The Docker image @"bcosc/arv-base-java"@ supplied here has the Java runtime environment, bwa, and samtools installed.
* Choose <i class="fa fa-fw fa-archive"></i> "Tutorial chromosome 19 reference (2463fa9efeb75e099685528b3b9071e0+438)":{{site.arvados_workbench_host}}/collections/2463fa9efeb75e099685528b3b9071e0+438 for the "reference_collection" parameter
* Choose <i class="fa fa-fw fa-archive"></i> "Tutorial sample exome (3229739b505d2b878b62aed09895a55a+142)":{{site.arvados_workbench_host}}/collections/3229739b505d2b878b62aed09895a55a+142 for the "sample" parameter
-For more information and examples for writing pipelines, see the "pipeline template reference":{{site.baseurl}}/api/schema/PipelineTemplate.html
+For more information and examples for writing pipelines, see the "pipeline template reference":{{site.baseurl}}/api/methods/pipeline_templates.html
h2. Re-using your pipeline run
* @"repository"@ is the name of a git repository to search for the script version. You can access a list of available git repositories on the Arvados Workbench in the *Repositories* page using the <span class="fa fa-lg fa-user"></span> <span class="caret"></span> top navigation menu icon.
* @"script_version"@ specifies the version of the script that you wish to run. This can be in the form of an explicit Git revision hash, a tag, or a branch (in which case it will use the HEAD of the specified branch). Arvados logs the script version that was used in the run, enabling you to go back and re-run any past job with the guarantee that the exact same code will be used as was used in the previous run.
* @"script"@ specifies the filename of the script to run. Crunch expects to find this in the @crunch_scripts/@ subdirectory of the Git repository.
-* @"runtime_constraints"@ describes the runtime environment required to run the job. These are described in the "job record schema":{{site.baseurl}}/api/schema/Job.html
+* @"runtime_constraints"@ describes the runtime environment required to run the job. These are described in the "job record schema":{{site.baseurl}}/api/methods/jobs.html
h2. Running your pipeline
Your new pipeline template should appear at the top of the Workbench "pipeline templates":{{site.arvados_workbench_host}}/pipeline_templates page. You can run your pipeline "using Workbench":tutorial-pipeline-workbench.html or the "command line.":{{site.baseurl}}/user/topics/running-pipeline-command-line.html
-For more information and examples for writing pipelines, see the "pipeline template reference":{{site.baseurl}}/api/schema/PipelineTemplate.html
+For more information and examples for writing pipelines, see the "pipeline template reference":{{site.baseurl}}/api/methods/pipeline_templates.html
projects / arvados.git / commitdiff