From f17319c645b30aaf976000134a18433d3a8adb19 Mon Sep 17 00:00:00 2001 From: Brett Smith Date: Fri, 15 Jul 2016 11:03:56 -0400 Subject: [PATCH] 9369: Copyedits throughout the CWL documentation. --- doc/sdk/cli/install.html.textile.liquid | 4 ++-- doc/user/cwl/cwl-runner.html.textile.liquid | 13 ++++++------- 2 files changed, 8 insertions(+), 9 deletions(-) diff --git a/doc/sdk/cli/install.html.textile.liquid b/doc/sdk/cli/install.html.textile.liquid index eff019a7fd..53821b5264 100644 --- a/doc/sdk/cli/install.html.textile.liquid +++ b/doc/sdk/cli/install.html.textile.liquid @@ -6,7 +6,7 @@ title: "Installation" ... -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 @@ -20,7 +20,7 @@ $ sudo apt-get install libcurl3 libcurl3-gnutls libcurl4 -h3. Option 1: Install from RubyGems and PyPi +h3. Option 1: Install from RubyGems and PyPI 
diff --git a/doc/user/cwl/cwl-runner.html.textile.liquid b/doc/user/cwl/cwl-runner.html.textile.liquid
index 917019ffd0..c00f475ad9 100644
--- a/doc/user/cwl/cwl-runner.html.textile.liquid
+++ b/doc/user/cwl/cwl-runner.html.textile.liquid
@@ -4,7 +4,7 @@ navsection: userguide
 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' %}
 
@@ -43,7 +43,7 @@ Server:
-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 @@ -108,8 +108,7 @@ qr1hi-8i9sb-fm2n3b1w0l6bskg 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. -

-~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner --local bwa-mem.cwl bwa-mem-input.yml
+
~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner --local bwa-mem.cwl bwa-mem-input.yml
 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
@@ -143,7 +142,7 @@ If you reference a local file which is not in @arv-mount@, then @arvados-cwl-run
 
 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  Run a pipeline... 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  Run a pipeline... on the Workbench Dashboard.
 
 
 
~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner --create-template bwa-mem.cwl
@@ -155,7 +154,7 @@ qr1hi-p5p6p-rjleou1dwr167v5
 

 
 
-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:
 
 
 
~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner --create-template bwa-mem.cwl bwa-mem-template.yml
@@ -295,4 +294,4 @@ Final process status is success
 

 
 
-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.
-- 
2.30.2