...
-Arvados CLI tools are written in Ruby and Python. To use the @arv@ command, you can either install the @arvados-cli@ gem via RubyGems or build and install the package from source. The @arv@ command also relies on other Arvados tools, you can either install the @arvados-python-client@ and @arvados-cwl-runner@ from PyPi or install the packages from source.
+Arvados CLI tools are written in Ruby and Python. To use the @arv@ command, you can either install the @arvados-cli@ gem via RubyGems or build and install the package from source. The @arv@ command also relies on other Arvados tools. To get those, you can either install the @arvados-python-client@ and @arvados-cwl-runner@ from PyPI or install the packages from source.
h3. Prerequisites: Ruby, Bundler, and curl libraries
</pre>
</notextile>
-h3. Option 1: Install from RubyGems and PyPi
+h3. Option 1: Install from RubyGems and PyPI
<notextile>
<pre>
title: Using Common Workflow Language
...
-The "Common Workflow Language (CWL)":http://commonwl.org is a multi-vendor open standard for describing analysis tools and workflows that are portable across a variety of platforms. CWL is the recommended way to develop and run Workflows for Arvados. Arvados supports the "CWL v1.0":http://commonwl.org/v1.0 specification.
+The "Common Workflow Language (CWL)":http://commonwl.org is a multi-vendor open standard for describing analysis tools and workflows that are portable across a variety of platforms. CWL is the recommended way to develop and run workflows for Arvados. Arvados supports the "CWL v1.0":http://commonwl.org/v1.0 specification.
{% include 'tutorial_expectations' %}
</code></pre>
</notextile>
-If this returns an error, contact the sysadmin of your cluster for assistance. Alternately, if you have Docker installed on your local workstation, you may follow the instructions above to install @arvados-cwl-runner@.
+If this returns an error, contact the sysadmin of your cluster for assistance. Alternatively, if you have Docker installed on your local workstation, you may follow the instructions above to install @arvados-cwl-runner@.
h3. Getting the example files
To run a workflow with local control, use @--local@. This means that the host where you run @arvados-cwl-runner@ will be responsible for submitting jobs. With @--local@, if you interrupt @arvados-cwl-runner@ or log out, the workflow will be terminated.
<notextile>
-<pre><code>
-~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --local bwa-mem.cwl bwa-mem-input.yml</span>
+<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --local bwa-mem.cwl bwa-mem-input.yml</span>
arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
2016-07-01 10:05:19 arvados.cwl-runner[16290] INFO: Pipeline instance qr1hi-d1hrv-92wcu6ldtio74r4
2016-07-01 10:05:28 arvados.cwl-runner[16290] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-2nzzfbuf9zjrj4g) is Queued
h2. Registering a workflow with Workbench
-Use @--create-template@ to register a CWL workflow with Arvados Workbench. This enables you to run Workflows by clicking on the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a pipeline...</span> on the Workbench Dashboard.
+Use @--create-template@ to register a CWL workflow with Arvados Workbench. This enables you to run workflows by clicking on the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a pipeline...</span> on the Workbench Dashboard.
<notextile>
<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --create-template bwa-mem.cwl</span>
</code></pre>
</notextile>
-You can provide a partial input file to set default values for the Workflow input parameters:
+You can provide a partial input file to set default values for the workflow input parameters:
<notextile>
<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --create-template bwa-mem.cwl bwa-mem-template.yml</span>
</code></pre>
</notextile>
-If you get the error @JavascriptException: Long-running script killed after 20 seconds.@ this may be due to the Dockerized Node.js engine taking too long to start. You may address this by installing @Node.js@ (@apt-get install nodejs@ on Debian or Ubuntu) locally or by providing a longer timeout, for example @cwltool --eval-timeout=40@ for a 40 second timeout.
+If you get the error @JavascriptException: Long-running script killed after 20 seconds.@ this may be due to the Dockerized Node.js engine taking too long to start. You may address this by installing Node.js locally (run @apt-get install nodejs@ on Debian or Ubuntu) or by specifying a longer timeout with the @--eval-timeout@ option. For example, run the workflow with @cwltool --eval-timeout=40@ for a 40-second timeout.