Merge remote-tracking branch 'origin/master' into 2049-run-job-from-workbench

[arvados.git] / doc / user / tutorials / tutorial-firstscript.html.textile.liquid

diff --git a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
index 2422bb2814f9ae9747f98745ce955e0d06212a24..4c49d19355119bff44d66e04dd538e00a1486651 100644 (file)
--- a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
@@ -10,9 +10,9 @@ h1. Writing a Crunch script
 
 In this tutorial, we will write the "hash" script demonstrated in the first tutorial.
 
-*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.basedoc}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.basedoc}}/user/getting_started/check-environment.html*
+*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. Setting up Git
 
@@ -21,20 +21,20 @@ As discussed in the previous tutorial, all Crunch scripts are managed through th
 First, you should do some basic configuration for git (you only need to do this the first time):
 
 <notextile>
-<pre><code>$ <span class="userinput">git config --global user.name "Your Name"</span>
-$ <span class="userinput">git config --global user.email you@example.com</span></code></pre>
+<pre><code>~$ <span class="userinput">git config --global user.name "Your Name"</span>
+~$ <span class="userinput">git config --global user.email <b>you</b>@example.com</span></code></pre>
 </notextile>
 
-On the Arvados Workbench, navigate to _Access %(rarr)&rarr;% Repositories._  You should see two repositories, one named "arvados" (under the *name* column) and a second with your user name.  Next to *name* is the column *push_url*.  Copy the *push_url* cell associated with your repository.  This should look like <code>git@git.{{ site.arvados_api_host }}:you.git</code>.
+On the Arvados Workbench, navigate to _Compute %(rarr)&rarr;% Code repositories._  You should see two repositories, one named "arvados" (under the *name* column) and a second with your user name.  Next to *name* is the column *push_url*.  Copy the *push_url* cell associated with your repository.  This should look like <notextile><code>git@git.{{ site.arvados_api_host }}:<b>you</b>.git</code></notextile>.
 
 Next, on the Arvados virtual machine, clone your git repository:
 
 <notextile>
-<pre><code>$ <span class="userinput">git clone git@git.{{ site.arvados_api_host }}:you.git</span>
-Cloning into 'you'...</code></pre>
+<pre><code>~$ <span class="userinput">git clone git@git.{{ site.arvados_api_host }}:<b>you</b>.git</span>
+Cloning into '<b>you</b>'...</code></pre>
 </notextile>
 
-This will create an git checkout in the directory called @you@.
+This will create an git checkout in the directory called *@you@*.
 
 {% include 'notebox_begin' %}
 For more information about using @git@, try
@@ -46,17 +46,17 @@ or <b>"click here to search Google for git tutorials":http://google.com/#q=git+t
 
 h2. Creating a Crunch script
 
-Start by entering the @you@ directory created by @git clone@.  Next create a subdirectory called @crunch_scripts@ and change to that directory:
+Start by entering the *@you@* directory created by @git clone@.  Next create a subdirectory called @crunch_scripts@ and change to that directory:
 
 <notextile>
-<pre><code>$ <span class="userinput">cd you</span>
-$ <span class="userinput">mkdir crunch_scripts</span>
-$ <span class="userinput">cd crunch_scripts</span></code></pre>
+<pre><code>~$ <span class="userinput">cd <b>you</b></span>
+~/<b>you</b>$ <span class="userinput">mkdir crunch_scripts</span>
+~/<b>you</b>$ <span class="userinput">cd crunch_scripts</span></code></pre>
 </notextile>
 
 Next, using @nano@ or your favorite Unix text editor, create a new file called @hash.py@ in the @crunch_scripts@ directory.
 
-notextile. <pre>$ <code class="userinput">nano hash.py</code></pre>
+notextile. <pre>~/<b>you</b>/crunch_scripts$ <code class="userinput">nano hash.py</code></pre>
 
 Add the following code to compute the md5 hash of each file in a collection:
 
@@ -64,16 +64,16 @@ Add the following code to compute the md5 hash of each file in a collection:
 
 Make the file executable:
 
-notextile. <pre><code>$ <span class="userinput">chmod +x hash.py</span></code></pre>
+notextile. <pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">chmod +x hash.py</span></code></pre>
 
 Next, add the file to @git@ staging.  This tells @git@ that the file should be included on the next commit.
 
-notextile. <pre><code>$ <span class="userinput">git add hash.py</span></code></pre>
+notextile. <pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">git add hash.py</span></code></pre>
 
 Next, commit your changes to git.  All staged changes are recorded into the local @git@ repository:
 
 <notextile>
-<pre><code>$ <span class="userinput">git commit -m"my first script"</span>
+<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">git commit -m"my first script"</span>
 [master (root-commit) 27fd88b] my first script
  1 file changed, 33 insertions(+)
  create mode 100755 crunch_scripts/hash.py</code></pre>
@@ -82,7 +82,7 @@ Next, commit your changes to git.  All staged changes are recorded into the loca
 Finally, upload your changes to the Arvados server:
 
 <notextile>
-<pre><code>$ <span class="userinput">git push origin master</span>
+<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">git push origin master</span>
 Counting objects: 4, done.
 Compressing objects: 100% (2/2), done.
 Writing objects: 100% (4/4), 682 bytes, done.
@@ -94,7 +94,7 @@ To git@git.qr1hi.arvadosapi.com:you.git
 You should now be able to run your script using Crunch, similar to how we did it in the "first tutorial.":tutorial-job1.html  The field @"script_version"@ should be @you:master@ to tell Crunch to run the script at the head of the "master" git branch, which you just uploaded.
 
 <notextile>
-<pre><code>$ <span class="userinput">cat &gt;the_job &lt;&lt;EOF
+<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cat &gt;~/the_job &lt;&lt;EOF
 {
  "script": "hash.py",
  "script_version": "you:master",
@@ -104,19 +104,19 @@ You should now be able to run your script using Crunch, similar to how we did it
  }
 }
 EOF</span>
-$ <span class="userinput">arv -h job create --job "$(cat the_job)"</span>
+~/<b>you</b>/crunch_scripts$ <span class="userinput">arv job create --job "$(cat ~/the_job)"</span>
 {
  ...
  "uuid":"qr1hi-xxxxx-xxxxxxxxxxxxxxx"
  ...
 }
-$ <span class="userinput">arv -h job get --uuid qr1hi-xxxxx-xxxxxxxxxxxxxxx</span>
+~/<b>you</b>/crunch_scripts$ <span class="userinput">arv job get --uuid qr1hi-xxxxx-xxxxxxxxxxxxxxx</span>
 {
  ...
  "output":"880b55fb4470b148a447ff38cacdd952+54",
  ...
 }
-$ <span class="userinput">arv keep get 880b55fb4470b148a447ff38cacdd952+54/md5sum.txt</span>
+~/<b>you</b>/crunch_scripts$ <span class="userinput">arv keep get 880b55fb4470b148a447ff38cacdd952+54/md5sum.txt</span>
 44b8ae3fde7a8a88d2f7ebd237625b4f var-GS000016015-ASM.tsv.bz2
 </code></pre>
 </notextile>