Merge branch 'master' into 2221-complete-docker

Conflicts:
	doc/user/topics/tutorial-job-debug.html.textile.liquid
	doc/user/tutorials/tutorial-keep.html.textile.liquid

diff --combined doc/install/client.html.textile.liquid
index 1e5151dbcf5165e1485c519f2d75d223a78e420c,b395d060f565c351502403ddc0f8dffd84b26ce3..2c3b6eb48ec9ca1932bd163561a5459333aa44b1
--- 1/doc/install/client.html.textile.liquid
--- 2/doc/install/client.html.textile.liquid
+++ b/doc/install/client.html.textile.liquid
@@@ -5,7 -5,7 +5,7 @@@ title: Install client librarie
  
  ...
  
- h1. Install client libraries
+ 
  
  h3. Python
  
@@@ -34,17 -34,3 +34,17 @@@ The arvados package includes the Ruby c
  {% include 'notebox_end' %}
  
  notextile. <pre><code>$ <span class="userinput">sudo gem install arvados arvados-cli</span></code></pre>
 +
 +h3. Perl
 +
 +{% include 'notebox_begin' %}
 +The Perl client library includes the @Arvados.pm@ module and submodules.
 +{% include 'notebox_end' %}
 +
 +<notextile>
 +<pre><code>$ <span class="userinput">cd arvados/sdk/perl</span>
 +$ <span class="userinput">perl Makefile.PL</span>
 +$ <span class="userinput">sudo make install</span>
 +</code></pre>
 +</notextile>
 +

diff --combined doc/user/topics/tutorial-job-debug.html.textile.liquid
index 3a3cbace550f7fe85b75b144a0fa8d65b07b13d1,0974e51697031449259f89221e4a0dc18e81658c..a28a793d47df725cec8e1d529dd8cf7960da2810
--- 1/doc/user/tutorials/tutorial-job-debug.html.textile.liquid
--- 2/doc/user/topics/tutorial-job-debug.html.textile.liquid
+++ b/doc/user/topics/tutorial-job-debug.html.textile.liquid
@@@ -1,18 -1,14 +1,14 @@@
  ---
  layout: default
  navsection: userguide
- navmenu: Tutorials
  title: "Debugging a Crunch script"
- 
  ...
  
- h1. Debugging a Crunch script
- 
  To test changes to a script by running a job, the change must be pushed into @git@, the job queued asynchronously, and the actual execution may be run on any compute server.  As a result, debugging a script can be difficult and time consuming.  This tutorial demonstrates using @arv-crunch-job@ to run your job in your local VM.  This avoids the job queue and allows you to execute the script from your uncomitted git tree.
  
  *This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
  
- This tutorial uses _you_ to denote your username.  Replace _you_ with your user name in all the following examples.
+ This tutorial uses *@you@* to denote your username.  Replace *@you@* with your user name in all the following examples.
  
  h2. Create a new script
  
@@@ -37,7 -33,7 +33,7 @@@ Instead of a git commit hash, we provid
  <pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cat &gt;~/the_job &lt;&lt;EOF
  {
   "script":"hello-world.py",
-  "script_version":"/home/you/you",
+  "script_version":"/home/<b>you</b>/<b>you</b>",
   "script_parameters":{}
  }
  EOF</span>
@@@ -46,7 -42,7 +42,7 @@@
  2013-12-12_21:36:42 qr1hi-8i9sb-okzukfzkpbrnhst 29827  node localhost - 1 slots
  2013-12-12_21:36:42 qr1hi-8i9sb-okzukfzkpbrnhst 29827  start
  2013-12-12_21:36:42 qr1hi-8i9sb-okzukfzkpbrnhst 29827  script hello-world.py
- 2013-12-12_21:36:42 qr1hi-8i9sb-okzukfzkpbrnhst 29827  script_version /home/you/you
+ 2013-12-12_21:36:42 qr1hi-8i9sb-okzukfzkpbrnhst 29827  script_version /home/<b>you</b>/<b>you</b>
  2013-12-12_21:36:42 qr1hi-8i9sb-okzukfzkpbrnhst 29827  script_parameters {}
  2013-12-12_21:36:42 qr1hi-8i9sb-okzukfzkpbrnhst 29827  runtime_constraints {"max_tasks_per_node":0}
  2013-12-12_21:36:42 qr1hi-8i9sb-okzukfzkpbrnhst 29827  start level 0
@@@ -101,7 -97,7 +97,7 @@@ EOF</span
  ~/<b>you</b>/crunch_scripts$ <span class="userinput">cat &gt;~/the_job &lt;&lt;EOF
  {
   "script":"hello-world-fixed.py",
-  "script_version":"/home/you/you",
+  "script_version":"/home/<b>you</b>/<b>you</b>",
   "script_parameters":{}
  }
  EOF</span>
@@@ -109,8 -105,8 +105,8 @@@
  2013-12-12_21:56:59 qr1hi-8i9sb-79260ykfew5trzl 31578  check slurm allocation
  2013-12-12_21:56:59 qr1hi-8i9sb-79260ykfew5trzl 31578  node localhost - 1 slots
  2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578  start
 -2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578  script hello-world.py
 +2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578  script hello-world-fixed.py
- 2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578  script_version /home/you/you
+ 2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578  script_version /home/<b>you</b>/<b>you</b>
  2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578  script_parameters {}
  2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578  runtime_constraints {"max_tasks_per_node":0}
  2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578  start level 0
@@@ -126,13 -122,11 +122,13 @@@
  2013-12-12_21:57:02 qr1hi-8i9sb-79260ykfew5trzl 31578  Freeze not implemented
  2013-12-12_21:57:02 qr1hi-8i9sb-79260ykfew5trzl 31578  collate
  2013-12-12_21:57:02 qr1hi-8i9sb-79260ykfew5trzl 31578  output 576c44d762ba241b0a674aa43152b52a+53
 +WARNING:root:API lookup failed for collection 576c44d762ba241b0a674aa43152b52a+53 (<class 'apiclient.errors.HttpError'>: <HttpError 404 when requesting https://qr1hi.arvadosapi.com/arvados/v1/collections/576c44d762ba241b0a674aa43152b52a%2B53?alt=json returned "Not Found">)
  2013-12-12_21:57:03 qr1hi-8i9sb-79260ykfew5trzl 31578  finish
 -2013-12-12_21:57:04 qr1hi-8i9sb-79260ykfew5trzl 31578  meta key is 9f937693334d0c9234ccc1f808ee7117+1761
  </code></pre>
  </notextile>
  
 +(The WARNING issued near the end of the script may be safely ignored here; it is the Arvados SDK letting you know that it could not find a collection named @576c44d762ba241b0a674aa43152b52a+53@ and that it is going to try looking up a block by that name instead.)
 +
  The job succeeded, with output in Keep object @576c44d762ba241b0a674aa43152b52a+53@.  Let's look at our output:
  
  <notextile>
@@@ -155,4 -149,3 +151,3 @@@ Read and write data to @/tmp/@ instead 
  
  notextile. <pre><code>~$ <span class="userinput">export KEEP_LOCAL_STORE=/tmp</span></code></pre>
  
- Next, "parallel tasks.":tutorial-parallel.html