X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/779c5400a4f376489f4abc8564f890f309ae3f20..eae48c31bb338689ec67fbc6a14a2e0b1fb5e3b6:/doc/user/tutorials/running-external-program.html.textile.liquid diff --git a/doc/user/tutorials/running-external-program.html.textile.liquid b/doc/user/tutorials/running-external-program.html.textile.liquid index ef4634ee74..a7682594c9 100644 --- a/doc/user/tutorials/running-external-program.html.textile.liquid +++ b/doc/user/tutorials/running-external-program.html.textile.liquid @@ -22,7 +22,7 @@ This will open the template record in an interactive text editor (as specified b * @"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. @@ -62,7 +62,7 @@ Test data is available in the "Arvados Tutorial":{{site.arvados_workbench_host}} * Choose "Tutorial chromosome 19 reference (2463fa9efeb75e099685528b3b9071e0+438)":{{site.arvados_workbench_host}}/collections/2463fa9efeb75e099685528b3b9071e0+438 for the "reference_collection" parameter * Choose "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