- user/tutorials/tutorial-firstscript.html.textile.liquid
- user/tutorials/tutorial-submit-job.html.textile.liquid
- user/topics/tutorial-parallel.html.textile.liquid
+ - user/topics/run-command.html.textile.liquid
- user/examples/crunch-examples.html.textile.liquid
- Query the metadata database:
- user/topics/tutorial-trait-search.html.textile.liquid
--- /dev/null
+"bwa-mem": {
+ "script": "run-command",
+ "script_version": "master",
+ "repository": "arvados",
+ "script_parameters": {
+ "command": [
+ "bwa",
+ "mem",
+ "-t",
+ "$(node.cores)",
+ "$(glob $(dir $(reference_collection))/*.fasta)",
+ "$(glob $(dir $(sample))/*_1.fastq)",
+ "$(glob $(dir $(sample))/*_2.fastq)"
+ ],
+ "task.foreach": ["samples", "pairs"],
+ "task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam"
+ "reference_collection": {
+ "required": true,
+ "dataclass": "Collection"
+ },
+ "samples": {
+ "required": true,
+ "dataclass": "Collection"
+ },
+ }
+}
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "run-command reference"
+...
+
+The @run-command@ crunch script provides a way to run a command over a dataset. Run-command is controlled through the script_parameters section of a pipeline component.
+
+<notextile>{% code 'run_command_example' as javascript %}</notextile>
+
+The script_parameters section consists of three parts:
+* The @command@ section defining how to build the command line of task
+* Special processing directives @task.foreach@ @task.cwd@ @task.vwd@ @task.stdin@ @task.stdout@
+* User-defined parameters