+If you need to capture intermediate results of a pipe, use the @tee@ command.
+
+h2. Running a shell script
+
+<notextile>
+<pre>
+$ <span class="userinput">echo 'echo hello world' > hello.sh</span>
+$ <span class="userinput">arv-run /bin/sh hello.sh</span>
+Upload local files: "hello.sh"
+Uploaded to qr1hi-4zz18-23u3hxugbm71qmn
+Running pipeline qr1hi-d1hrv-slcnhq5czo764b1
+[...]
+ 0 stderr run-command: /bin/sh /keep/5d3a4131b7d8f233f2a917d8a5c3c2b2+52/hello.sh
+ 0 stderr hello world
+ 0 stderr run-command: completed with exit code 0 (success)
+[...]
+</pre>
+</notextile>
+
+h2. Additional options
+
+* @--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.
+* @--no-wait@ : Do not wait and display logs after submitting command, just exit.
+
+h2. Putting it all together: bwa mem