[ARVADOS] updated: 7bd12f51c864ec78fc93f0fa95acf796a4999afc
git at public.curoverse.com
git at public.curoverse.com
Mon Jul 13 15:12:16 EDT 2015
Summary of changes:
.../app/controllers/virtual_machines_controller.rb | 10 +
.../views/users/_manage_virtual_machines.html.erb | 12 +
.../app/views/virtual_machines/webshell.html.erb | 49 +
apps/workbench/config/application.default.yml | 10 +
apps/workbench/config/routes.rb | 1 +
apps/workbench/public/webshell/README | 3 +
apps/workbench/public/webshell/enabled.gif | Bin 0 -> 847 bytes
apps/workbench/public/webshell/keyboard.html | 62 +
apps/workbench/public/webshell/keyboard.png | Bin 0 -> 808 bytes
apps/workbench/public/webshell/shell_in_a_box.js | 4835 ++++++++++++++++++++
apps/workbench/public/webshell/styles.css | 272 ++
doc/_config.yml | 2 +
doc/images/add-new-repository.png | Bin 0 -> 42533 bytes
doc/images/repositories-panel.png | Bin 0 -> 32812 bytes
doc/user/reference/api-tokens.html.textile.liquid | 2 +-
.../add-new-repository.html.textile.liquid | 40 +
.../tutorial-firstscript.html.textile.liquid | 5 +-
.../tutorial-submit-job.html.textile.liquid | 26 +-
docker/build_tools/Makefile | 4 +-
docker/jobs/Dockerfile | 29 +-
docker/{base => jobs}/apt.arvados.org.list | 0
21 files changed, 5331 insertions(+), 31 deletions(-)
create mode 100644 apps/workbench/app/views/virtual_machines/webshell.html.erb
create mode 100644 apps/workbench/public/webshell/README
create mode 100644 apps/workbench/public/webshell/enabled.gif
create mode 100644 apps/workbench/public/webshell/keyboard.html
create mode 100644 apps/workbench/public/webshell/keyboard.png
create mode 100644 apps/workbench/public/webshell/shell_in_a_box.js
create mode 100644 apps/workbench/public/webshell/styles.css
create mode 100644 doc/images/add-new-repository.png
create mode 100644 doc/images/repositories-panel.png
create mode 100644 doc/user/tutorials/add-new-repository.html.textile.liquid
copy docker/{base => jobs}/apt.arvados.org.list (100%)
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commit 7bd12f51c864ec78fc93f0fa95acf796a4999afc
Author: radhika <radhika at curoverse.com>
Date: Mon Jul 13 15:10:37 2015 -0400
6014: Add "add new repository" page to create a tutorial repository, and update the tutorial-submit-job page to use the tutorial repository.
diff --git a/doc/_config.yml b/doc/_config.yml
index 48a6a01..c24f0a6 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -44,6 +44,8 @@ navbar:
- Run a pipeline on the command line:
- user/topics/running-pipeline-command-line.html.textile.liquid
- user/topics/arv-run.html.textile.liquid
+ - Working with Arvados Repositories:
+ - user/tutorials/add-new-repository.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/images/add-new-repository.png b/doc/images/add-new-repository.png
new file mode 100644
index 0000000..4ec2c2e
Binary files /dev/null and b/doc/images/add-new-repository.png differ
diff --git a/doc/images/repositories-panel.png b/doc/images/repositories-panel.png
new file mode 100644
index 0000000..3e12860
Binary files /dev/null and b/doc/images/repositories-panel.png differ
diff --git a/doc/user/reference/api-tokens.html.textile.liquid b/doc/user/reference/api-tokens.html.textile.liquid
index ab1cdc6..f9f8af8 100644
--- a/doc/user/reference/api-tokens.html.textile.liquid
+++ b/doc/user/reference/api-tokens.html.textile.liquid
@@ -6,7 +6,7 @@ title: "Getting an API token"
The Arvados API token is a secret key that enables the @arv@ command line client to access Arvados with the proper permissions.
-Access the Arvados Workbench using this link: "{{site.arvados_workbench_host}}/":{{site.arvados_workbench_host}}/ (Replace @{{ site.arvados_api_host }}@ with the hostname of your local Arvados instance if necessary.)
+Access the Arvados Workbench using this link: "{{site.arvados_workbench_host}}/":{{site.arvados_workbench_host}}/ (Replace the hostname portion with the hostname of your local Arvados instance if necessary.)
Open a shell on the system where you want to use the Arvados client. This may be your local workstation, or an Arvados virtual machine accessed with SSH (instructions for "Unix":{{site.baseurl}}/user/getting_started/ssh-access-unix.html#login or "Windows":{{site.baseurl}}/user/getting_started/ssh-access-windows.html#login).
diff --git a/doc/user/tutorials/add-new-repository.html.textile.liquid b/doc/user/tutorials/add-new-repository.html.textile.liquid
new file mode 100644
index 0000000..a4ccbe1
--- /dev/null
+++ b/doc/user/tutorials/add-new-repository.html.textile.liquid
@@ -0,0 +1,40 @@
+---
+layout: default
+navsection: userguide
+title: Add 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.
+
+{% include 'tutorial_expectations' %}
+
+h2. Setting up Git
+
+Before you start using Git and arvados repositories, 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 $USER at example.com</span></code></pre>
+</notextile>
+
+h2. Add "tutorial" repository
+
+On the Arvados Workbench, click on the dropdown menu icon <span class="fa fa-lg fa-user"></span> <span class="caret"></span> in the upper right corner of the top navigation menu to access the user settings menu, and click on the menu item *Manage account* to go to the account management page.
+
+On the *Manage account* page, you will see *Repositories* panel with a *Add new repository* button.
+
+!{{ site.baseurl }}/images/repositories-panel.png!
+
+Click the *Add new Repository* button to open the popup to add a new arvados repository. You will see a text box where you can enter the name of the repository. Enter *tutorial* in this text box and click on *Create*.
+
+{% include 'notebox_begin' %}
+The name you enter here can only be of the format *a letter followed by alphanumeric characters*.
+{% include 'notebox_end' %}
+
+!{{ site.baseurl }}/images/add-new-repository.png!
+
+This will create a new repository with the name @$USER/tutorial@ with the URL <notextile><code>git at git.{{ site.arvados_api_host }}:$USER/tutorial.git</code></notextile>
+
+Back in the *Repositories* panel in the *manage account* page, you should see the @$USER/tutorial@ repository listed in the name column with the URL <notextile><code>git at git.{{ site.arvados_api_host }}:$USER/tutorial.git</code></notextile>.
+
+You are now ready to use this *tutorial* repository to run your crunch scripts.
diff --git a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
index adf4da1..bf73c8c 100644
--- a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
@@ -11,10 +11,11 @@ This tutorial demonstrates how to write a script using Arvados Python SDK. The
This tutorial uses @$USER@ to denote your username. Replace @$USER@ with your user name in all the following examples.
-Start by creating a directory called @$USER@ . Next, create a subdirectory called @crunch_scripts@ and change to that directory:
+Start by creating a directory called @tutorial@ in your home directory. Next, create a subdirectory called @crunch_scripts@ and change to that directory:
<notextile>
-<pre><code>~$ <span class="userinput">mkdir -p tutorial/crunch_scripts</span>
+<pre><code>~$ <span class="userinput">cd $HOME</span>
+~$ <span class="userinput">mkdir -p tutorial/crunch_scripts</span>
~$ <span class="userinput">cd tutorial/crunch_scripts</span></code></pre>
</notextile>
diff --git a/doc/user/tutorials/tutorial-submit-job.html.textile.liquid b/doc/user/tutorials/tutorial-submit-job.html.textile.liquid
index 3d58fad..eaafe96 100644
--- a/doc/user/tutorials/tutorial-submit-job.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-submit-job.html.textile.liquid
@@ -11,7 +11,9 @@ This tutorial demonstrates how to create a pipeline to run your crunch script on
This tutorial uses @$USER@ to denote your username. Replace @$USER@ with your user name in all the following examples.
-h2. Setting up Git
+Also, this tutorial uses the @tutorial@ arvados repository created in "Add new arvados repository":add-new-repository.html as the example repository.
+
+h2. Clone arvados repository
All Crunch scripts are managed through the Git revision control system. Before you start using Git, you should do some basic configuration (you only need to do this the first time):
@@ -22,17 +24,17 @@ All Crunch scripts are managed through the Git revision control system. Before
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 *Manage account* to go to the account management page.
-On the *Manage account* page, you will see *Repositories* panel. In this panel, you should see a repository with your user name 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>git at git.{{ site.arvados_api_host }}:$USER/$USER.git</code></notextile>.
+On the *Manage account* page, you will see *Repositories* panel. In this panel, you should see the @$USER/tutorial@ repository listed in the *name* column. Next to *name* is the column *URL*. Copy the *URL* value associated with your repository. This should look like <notextile><code>git at git.{{ site.arvados_api_host }}:$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 git at git.{{ site.arvados_api_host }}:$USER/$USER.git</span>
-Cloning into '$USER'...</code></pre>
+~$ <span class="userinput">git clone git at git.{{ site.arvados_api_host }}:$USER/tutorial.git</span>
+Cloning into 'tutorial'...</code></pre>
</notextile>
-This will create a Git repository in the directory called @$USER@ in your home directory. Say yes when prompted to continue with connection.
+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.
{% include 'notebox_begin' %}
@@ -45,7 +47,7 @@ or *"search Google for Git tutorials":http://google.com/#q=git+tutorial*.
h2. Creating a Crunch script
-Start by entering the @$USER@ directory created by @git clone at . Next create a subdirectory called @crunch_scripts@ and change to that directory:
+Start by entering the @tutorial@ directory created by @git clone at . Next create a subdirectory called @crunch_scripts@ and change to that directory:
<notextile>
<pre><code>~$ <span class="userinput">cd $USER</span>
@@ -55,7 +57,7 @@ Start by entering the @$USER@ directory created by @git clone at . Next create a s
Next, using @nano@ or your favorite Unix text editor, create a new file called @hash.py@ in the @crunch_scripts@ directory.
-notextile. <pre>~/$USER/crunch_scripts$ <code class="userinput">nano hash.py</code></pre>
+notextile. <pre>~/tutorial/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 (if you already completed "Writing a Crunch script":tutorial-firstscript.html you can just copy the @hash.py@ file you created previously.)
@@ -63,16 +65,16 @@ Add the following code to compute the MD5 hash of each file in a collection (if
Make the file executable:
-notextile. <pre><code>~/$USER/crunch_scripts$ <span class="userinput">chmod +x hash.py</span></code></pre>
+notextile. <pre><code>~/tutorial/crunch_scripts$ <span class="userinput">chmod +x hash.py</span></code></pre>
Next, add the file to the staging area. This tells @git@ that the file should be included on the next commit.
-notextile. <pre><code>~/$USER/crunch_scripts$ <span class="userinput">git add hash.py</span></code></pre>
+notextile. <pre><code>~/tutorial/crunch_scripts$ <span class="userinput">git add hash.py</span></code></pre>
Next, commit your changes. All staged changes are recorded into the local git repository:
<notextile>
-<pre><code>~/$USER/crunch_scripts$ <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>
@@ -81,12 +83,12 @@ Next, commit your changes. All staged changes are recorded into the local git r
Finally, upload your changes to the Arvados server:
<notextile>
-<pre><code>~/$USER/crunch_scripts$ <span class="userinput">git push origin master</span>
+<pre><code>~/tutorial/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.
Total 4 (delta 0), reused 0 (delta 0)
-To git at git.qr1hi.arvadosapi.com:$USER/$USER.git
+To git at git.qr1hi.arvadosapi.com:$USER/tutorial.git
* [new branch] master -> master</code></pre>
</notextile>
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