4042: Start working on run-command reference page.

diff --git a/doc/_config.yml b/doc/_config.yml
index 3301207250710e9d706d4177c2f12caa3ec257f9..61bfb6f85c2ecd7d5a5d21137f4bda4bb4c7b023 100644 (file)
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -39,6 +39,7 @@ navbar:
       - 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

diff --git a/doc/_includes/_run_command_example.liquid b/doc/_includes/_run_command_example.liquid
new file mode 100644 (file)
index 0000000..6de156d
--- /dev/null
+++ b/doc/_includes/_run_command_example.liquid
@@ -0,0 +1,26 @@
+"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"
+        },
+    }
+}

diff --git a/doc/user/topics/run-command.html.textile.liquid b/doc/user/topics/run-command.html.textile.liquid
new file mode 100644 (file)
index 0000000..1a2616b
--- /dev/null
+++ b/doc/user/topics/run-command.html.textile.liquid
@@ -0,0 +1,14 @@
+---
+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