[ARVADOS] created: 39c9193f03471aa7826769b34d6b55890a2c98a3

Tue Aug 18 11:25:46 EDT 2015

at  39c9193f03471aa7826769b34d6b55890a2c98a3 (commit)


commit 39c9193f03471aa7826769b34d6b55890a2c98a3
Author: Bryan Cosca <bcosc at curoverse.com>
Date:   Tue Aug 18 11:25:14 2015 -0400

    6862: Added a quick guide to git, from git clone to git push.

diff --git a/doc/_config.yml b/doc/_config.yml
index f21fdee..55e71ec 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -48,6 +48,7 @@ navbar:
       - user/topics/arv-run.html.textile.liquid
     - Working with Arvados Repositories:
       - user/tutorials/add-new-repository.html.textile.liquid
+      - user/tutorials/git-arvados-guide.html.textile.liquid
     - Develop a new pipeline:
       - user/tutorials/intro-crunch.html.textile.liquid
       - user/tutorials/running-external-program.html.textile.liquid
diff --git a/doc/_includes/_tutorial_git_repo_expectations.liquid b/doc/_includes/_tutorial_git_repo_expectations.liquid
new file mode 100644
index 0000000..57c5553
--- /dev/null
+++ b/doc/_includes/_tutorial_git_repo_expectations.liquid
@@ -0,0 +1,3 @@
+{% include 'notebox_begin' %}
+This tutorial assumes that you have a working Arvados repository. If you do not have a repository created, you can follow the "Adding a new repository":{{site.baseurl}}/user/tutorials/add-new-repository.html page. We will use the *$USER/tutorial* repository created in that page as the example.
+{% include 'notebox_end' %}
diff --git a/doc/user/tutorials/add-new-repository.html.textile.liquid b/doc/user/tutorials/add-new-repository.html.textile.liquid
index 762278a..d2a17a4 100644
--- a/doc/user/tutorials/add-new-repository.html.textile.liquid
+++ b/doc/user/tutorials/add-new-repository.html.textile.liquid
@@ -1,7 +1,7 @@
 ---
 layout: default
 navsection: userguide
-title: Adding a new arvados repository
+title: Adding a new Arvados repository
 ...
 
 Arvados repositories are managed through the Git revision control system. You can use these repositories to store your crunch scripts and run them in the arvados cluster.
diff --git a/doc/user/tutorials/git-arvados-guide.html.textile.liquid b/doc/user/tutorials/git-arvados-guide.html.textile.liquid
new file mode 100644
index 0000000..482d8d5
--- /dev/null
+++ b/doc/user/tutorials/git-arvados-guide.html.textile.liquid
@@ -0,0 +1,84 @@
+---
+layout: default
+navsection: userguide
+title: Working with an Arvados git repository
+...
+
+Working with an Arvados git repository is analogous to working with other public repositories. If you are already familiar with git, feel free to skip this part of the documentation.
+
+This tutorial describes how to work with a new Arvados git repository. It will show you how to upload custom scripts to a remote Arvados repository, so you can use it in Arvados pipelines.
+
+{% include 'tutorial_expectations' %}
+
+{% include 'tutorial_git_repo_expectations' %}
+
+h2. Cloning an Arvados repository
+
+Before you start using Git, you should do some basic configuration (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 $USER at example.com</span></code></pre>
+</notextile>
+
+On the Arvados Workbench, click on the dropdown menu icon <span class="fa fa-lg fa-user"></span> <span class="caret"></span> in the upper right corner of the top navigation menu to access the user settings menu, and click on the menu item *Repositories*. In the *Repositories* page, you should see the @$USER/tutorial@ repository listed in the *name* column.  Next to *name* is the column *URL*. Copy the *URL* value associated with your repository.  This should look like <notextile><code>https://git.{{ site.arvados_api_host }}/$USER/tutorial.git</code></notextile>. Alternatively, you can use <notextile><code>git at git.{{ site.arvados_api_host }}:$USER/tutorial.git</code></notextile>
+
+Next, on the Arvados virtual machine, clone your Git repository:
+
+<notextile>
+<pre><code>~$ <span class="userinput">cd $HOME</span> # (or wherever you want to install)
+~$ <span class="userinput">git clone https://git.{{ site.arvados_api_host }}/$USER/tutorial.git</span>
+Cloning into 'tutorial'...</code></pre>
+</notextile>
+
+This will create a Git repository in the directory called @tutorial@ in your home directory. Say yes when prompted to continue with connection.
+Ignore any warning that you are cloning an empty repository.
+
+*Note:* If you are prompted for username and password when you try to git clone using this command, you may first need to update your git configuration. Execute the following commands to update your git configuration.
+
+<notextile>
+<pre>
+<code>~$ <span class="userinput">git config 'credential.https://git.{{ site.arvados_api_host }}/.username' none</span></code>
+<code>~$ <span class="userinput">git config 'credential.https://git.{{ site.arvados_api_host }}/.helper' '!cred(){ cat >/dev/null; if [ "$1" = get ]; then echo password=$ARVADOS_API_TOKEN; fi; };cred'</span></code>
+</pre>
+</notextile>
+
+h2. Creating a git branch
+
+<notextile>
+<pre><code>~$ <span class="userinput">cd tutorial</span>
+<span class="userinput">git checkout -b tutorial_branch</span>
+</code></pre>
+</notextile>
+
+h2. Adding a script to git
+
+First, create a new file in the local repository.
+
+<notextile>
+<pre><code>~$ <span class="userinput">echo 'hello world' > tutorial.txt</span>
+</code></pre>
+</notextile>
+
+Next, add the new file to the git index.
+
+<notextile>
+<pre><code>~$ <span class="userinput">git add tutorial.txt</span>
+</code></pre>
+</notextile>
+
+Next, commit all the changes to the local repository, along with a message of what you've accomplished.
+
+<notextile>
+<pre><code>~$ <span class="userinput">git commit -a -m "Added tutorial.txt"</span>
+</code></pre>
+</notextile>
+
+Next, push the changes in the local repository to the remote repository.
+
+<notextile>
+<pre><code>~$ <span class="userinput">git push origin tutorial_branch</span>
+</code></pre>
+</notextile>
+
+Although this tutorial showed how to add a text file to Arvados, this tutorial should also show the necessary steps for adding your custom bash, R, or python scripts to an Arvados repository.
diff --git a/doc/user/tutorials/tutorial-submit-job.html.textile.liquid b/doc/user/tutorials/tutorial-submit-job.html.textile.liquid
index a6edc7d..dc1c849 100644
--- a/doc/user/tutorials/tutorial-submit-job.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-submit-job.html.textile.liquid
@@ -49,17 +49,17 @@ For more information about using Git, try
 
 notextile. <pre><code>$ <span class="userinput">man gittutorial</span></code></pre>
 
-or *"search Google for Git tutorials":http://google.com/#q=git+tutorial*.
+or go to our "Working with an Arvados Git Repository page":{{site.baseurl}}/user/tutorials/add-new-repository.html, or *"search Google for Git tutorials":http://google.com/#q=git+tutorial*.
 {% include 'notebox_end' %}
 
 h2. Creating a Crunch script
 
-Start by entering the @tutorial@ directory created by @git clone at .  Next create a subdirectory called @crunch_scripts@ and change to that directory:
+Start by entering the @tutorial@ directory created by @git clone at . Next, create a subdirectory called @crunch_scripts@ and change to that directory:
 
 <notextile>
-<pre><code>~$ <span class="userinput">cd $USER</span>
-~/$USER$ <span class="userinput">mkdir crunch_scripts</span>
-~/$USER$ <span class="userinput">cd crunch_scripts</span></code></pre>
+<pre><code>>~$ <span class="userinput">cd tutorial</span>
+~/tutorial$ <span class="userinput">mkdir crunch_scripts</span>
+~/tutorial$ <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.
@@ -81,7 +81,7 @@ notextile. <pre><code>~/tutorial/crunch_scripts$ <span class="userinput">git add
 Next, commit your changes.  All staged changes are recorded into the local git repository:
 
 <notextile>
-<pre><code>~/tutorial/crunch_scripts$ <span class="userinput">git commit -m"my first script"</span>
+<pre><code>~/tutorial/crunch_scripts$ <span class="userinput">git commit -m "my first script"</span>
 [master (root-commit) 27fd88b] my first script
  1 file changed, 45 insertions(+)
  create mode 100755 crunch_scripts/hash.py</code></pre>

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