Merge branch '8784-dir-listings'

[arvados.git] / doc / user / topics / arv-run.html.textile.liquid

diff --git a/doc/user/topics/arv-run.html.textile.liquid b/doc/user/topics/arv-run.html.textile.liquid
index 300ff2ff0431185cba11fa0d696c21f3dbe4c4db..9752ca7d2b49d1afb077f63d652a2c2835ce2d37 100644 (file)
--- a/doc/user/topics/arv-run.html.textile.liquid
+++ b/doc/user/topics/arv-run.html.textile.liquid
@@ -3,6 +3,15 @@ layout: default
 navsection: userguide
 title: "Using arv-run"
 ...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+{% include 'crunch1only_begin' %}
+On those sites, the features described here are not yet implemented.
+{% include 'crunch1only_end' %}
 
 The @arv-run@ command enables you create Arvados pipelines at the command line that fan out to multiple concurrent tasks across Arvados compute nodes.
 
@@ -43,6 +52,8 @@ h2. Parallel tasks
 
 <notextile>
 <pre>
+$ <span class="userinput">cd ~/keep/by_id/3229739b505d2b878b62aed09895a55a+142</span>
+$ <span class="userinput">ls *.fastq</span>
 HWI-ST1027_129_D0THKACXX.1_1.fastq  HWI-ST1027_129_D0THKACXX.1_2.fastq
 $ <span class="userinput">arv-run grep -H -n ATTGGAGGAAAGATGAGTGAC -- *.fastq</span>
 Running pipeline qr1hi-d1hrv-mg3bju0u7r6w241
@@ -69,30 +80,14 @@ You may use standard input (@<@) and standard output (@>@) redirection.  This wi
 
 (Note: because the syntax is designed to mimic standard shell syntax, it is necessary to quote the metacharacters @<@, @>@ and @|@ as either @\<@, @\>@ and @\|@ or @'<'@, @'>'@ and @'|'@.)
 
-<notextile>
-<pre>
-$ <span class="userinput">arv-run grep -H -n ATTGGAGGAAAGATGAGTGAC \< *.fastq \> output.txt</span>
-[...]
- 1 stderr run-command: grep -H -n ATTGGAGGAAAGATGAGTGAC < /keep/3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_1.fastq > output.txt
- 2 stderr run-command: grep -H -n ATTGGAGGAAAGATGAGTGAC < /keep/3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_2.fastq > output.txt
- 2 stderr run-command: completed with exit code 0 (success)
- 2 stderr run-command: the following output files will be saved to keep:
- 2 stderr run-command: 121 ./output.txt
- 2 stderr run-command: start writing output to keep
- 1 stderr run-command: completed with exit code 0 (success)
- 1 stderr run-command: the following output files will be saved to keep:
- 1 stderr run-command: 363 ./output.txt
- 1 stderr run-command: start writing output to keep
- 2 stderr upload wrote 121 total 121
- 1 stderr upload wrote 363 total 363
-[..]
-</pre>
-</notextile>
+{% include 'arv_run_redirection' %}
 
 You may use "run-command":run-command.html parameter substitution in the output file name to generate different filenames for each task:
 
 <notextile>
 <pre>
+$ <span class="userinput">cd ~/keep/by_id/3229739b505d2b878b62aed09895a55a+142</span>
+$ <span class="userinput">ls *.fastq</span>
 $ <span class="userinput">arv-run grep -H -n ATTGGAGGAAAGATGAGTGAC \< *.fastq \> '$(task.uuid).txt'</span>
 [...]
  1 stderr run-command: grep -H -n ATTGGAGGAAAGATGAGTGAC < /keep/3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_1.fastq > qr1hi-ot0gb-hmmxf2zubfpmhfk.txt
@@ -117,6 +112,8 @@ Multiple commands may be connected by pipes and execute in the same container:
 
 <notextile>
 <pre>
+$ <span class="userinput">cd ~/keep/by_id/3229739b505d2b878b62aed09895a55a+142</span>
+$ <span class="userinput">ls *.fastq</span>
 $ <span class="userinput">arv-run cat -- *.fastq \| grep -H -n ATTGGAGGAAAGATGAGTGAC \> output.txt</span>
 [...]
  1 stderr run-command: cat /keep/3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_1.fastq | grep -H -n ATTGGAGGAAAGATGAGTGAC > output.txt
@@ -146,10 +143,10 @@ Running pipeline qr1hi-d1hrv-slcnhq5czo764b1
 
 h2. Additional options
 
-* @--docker-image IMG@ : By default, commands run inside a Docker container created from the latest "arvados/jobs" Docker image.  Use this option to specify a different image to use.  Note: the Docker image must be uploaded to Arvados using @arv keep docker@.
+* @--docker-image IMG@ : By default, commands run based in a container created from the @default_docker_image_for_jobs@ setting on the API server.  Use this option to specify a different image to use.  Note: the Docker image must be uploaded to Arvados using @arv keep docker@.
 * @--dry-run@ : Print out the final Arvados pipeline generated by @arv-run@ without submitting it.
 * @--local@ : By default, the pipeline will be submitted to your configured Arvados instance.  Use this option to run the command locally using @arv-run-pipeline-instance --run-jobs-here@.
-* @--ignore-rcode@ : Some commands use non-zero exit codes to indicate nonfatal conditions (e.g. @grep@ returns 1 when no match is found).  Set this to indicate that commands that return non-zero return codes should not be considered failed.
+* @--ignore-rcode@ : Some commands use non-zero exit codes to indicate nonfatal conditions (e.g., @grep@ returns 1 when no match is found).  Set this to indicate that commands that return non-zero return codes should not be considered failed.
 * @--no-wait@ : Do not wait and display logs after submitting command, just exit.
 
 h2. Putting it all together: bwa mem