[ARVADOS] updated: 10898768160571a6963066d8e7236f89b3e0b29d
git at public.curoverse.com
git at public.curoverse.com
Tue Jul 8 15:03:46 EDT 2014
Summary of changes:
crunch_scripts/run-command | 94 +++++++++++++++------
doc/images/workbench-dashboard.png | Bin 0 -> 44822 bytes
.../getting_started/workbench.html.textile.liquid | 4 +-
...tutorial-pipeline-workbench.html.textile.liquid | 24 +++---
4 files changed, 83 insertions(+), 39 deletions(-)
create mode 100644 doc/images/workbench-dashboard.png
via 10898768160571a6963066d8e7236f89b3e0b29d (commit)
via d23fba84b810714ec2ab41a1501a39a5c665dcd4 (commit)
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via 8793c9cfb3b2e1a9c9ddadbfa7809598c07e27b2 (commit)
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via db1957ae42446d4e630800391c113b942c219227 (commit)
via d0fe5e9f95b45580d1d234a5adbe34705c7be1ff (commit)
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commit 10898768160571a6963066d8e7236f89b3e0b29d
Merge: 8793c9c d23fba8
Author: radhika <radhika at curoverse.com>
Date: Tue Jul 8 14:44:04 2014 -0400
Merge branch 'master' into 3203-workbench-tutorial
commit 8793c9cfb3b2e1a9c9ddadbfa7809598c07e27b2
Author: radhika <radhika at curoverse.com>
Date: Tue Jul 8 14:42:26 2014 -0400
3203: Update the pipeline tutorial page to run pipeline from a project.
diff --git a/doc/user/getting_started/workbench.html.textile.liquid b/doc/user/getting_started/workbench.html.textile.liquid
index 8140bba..ccfdb82 100644
--- a/doc/user/getting_started/workbench.html.textile.liquid
+++ b/doc/user/getting_started/workbench.html.textile.liquid
@@ -10,6 +10,6 @@ Access the Arvados beta test instance available using this link:
If you are accessing Arvados for the first time, you will be asked to log in using a Google account. Arvados uses only your name and email address from Google services for identification, and will never access any personal information. Once you are logged in, the Workbench page may indicate your account status is *New / inactive*. If this is the case, contact the administrator of the Arvados instance to activate your account.
-Once your account is active, logging in to the Workbench will present you with a system status dashboard. This gives a summary of data, configuration, and activity in the Arvados instance. The dashboard will display a welcome message if you have not yet created any projects. Create a new project by clicking on the <span class="btn-primary glyphicon-plus"> Add new project</span> button in the *My projects* panel in the dashboard.
+Once your account is active, logging in to the Workbench will present you with a system status dashboard. This gives a summary of data, configuration, and activity in the Arvados instance. The dashboard will display a welcome message if you have not yet created any projects. Create a new project by clicking on the <span class="btn btn-primary glyphicon-plus"> Add new project</span> button in the *My projects* panel in the dashboard.
!{{ site.baseurl }}/images/workbench-dashboard.png!
diff --git a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
index 277b966..5f98c8c 100644
--- a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
@@ -6,17 +6,21 @@ title: "Running a pipeline using Workbench"
notextile. <div class="spaced-out">
-# Go to "Collections":https://{{ site.arvados_workbench_host }}/collections (*Data* %(rarr)→% *Collections (data files)*).
-# On the Collections page, go to the search box <span class="glyphicon glyphicon-search"></span> and search for "tutorial".
-# The results should include a collection with the contents *var-GS000016015-ASM.tsv.bz2*.
-# Click on the check box to the left of *var-GS000016015-ASM.tsv.bz2*. This puts the collection in your persistent selection list. You can click on the paperclip <span class="glyphicon glyphicon-paperclip"></span> in the upper right to review your current selections.
-# Go to "Pipeline templates":https://{{ site.arvados_workbench_host }}/pipeline_templates (*Compute* %(rarr)→% *Pipeline templates*).
-# Look for a pipeline named *Tutorial pipeline*.
-# Click on the play button <span class="glyphicon glyphicon-play"></span> to the left of *Tutorial pipeline*. This will take you to a new page to configure the pipeline.
-# Under the *parameter* column, look for *input*. Set the value of *input* by clicking on *none* to get a selection popup. The collection that you selected in step 4 will be at the top of that pulldown menu. Select that collection in the pulldown menu.
-# You can now click on the *Run pipeline* button in the upper right to start the pipeline. A new page shows the pipeline status, queued to run.
+# If you have not yet created any projects, first create a new project to save your work. Please see "Accessing Arvados Workbench":{{site.baseurl}}/user/getting_started/workbench.html page for details. If you already have created a project for your work, go to the project by clicking on the project in *My projects* panel.
+# Click on the <span class="btn btn-primary glyphicon-plus"> Add data...</span> button.
+# In the *Add data to project* popup window, enter *tutorial* in the search box.
+# The results should include a *tutorial* collection.
+# Click on this collection and verify that it is the collection *var-GS000016015-ASM.tsv.bz2*.
+# Click on the <span class="btn btn-primary"> Add </span> button in the popup. This adds the *var-GS000016015-ASM.tsv.bz2* collection to your project.
+# Click on the <span class="btn btn-primary glyphicon-gear"> Run a pipeline... </span> button
+# In the *Choose a pipeline to run* popup window, enter *tutorial* in the search box.
+# The result should include *Tutorial pipeline* template.
+# Click on this template and the click on <span class="btn btn-primary"> Next: choose inputs </span> button. This will take you to a new page to configure the pipeline instance.
+# In the *Inputs* tab, click on <span class="btn btn-primary"> Choose </span> button
+# In the *Choose a dataset* popup, click on the *tutorial* collection and click on <span class="btn btn-primary"> OK </span> button.
+# You can now run this pipeline by clicking on the <span class="btn btn-primary"> Run </span> button.
# The page refreshes automatically every 15 seconds. You should see the pipeline running, and then finish successfully.
-# Once the pipeline is finished, click on the link under the *output* column. This will take you to the collection page for the output of this pipeline.
+# Once the pipeline is finished, click on the *Show output files* button. This will take you to the collection page for the output of this pipeline.
# Click on *md5sum.txt* to see the actual file that is the output of this pipeline.
# Go back to the collection page for the result. Click on the *Provenance graph* tab to see a graph illustrating the collections and scripts that were used to generate this file.
commit db1957ae42446d4e630800391c113b942c219227
Author: radhika <radhika at curoverse.com>
Date: Tue Jul 8 13:29:55 2014 -0400
3203: Update "Accessing Arvados Workbench" page.
diff --git a/doc/images/workbench-dashboard.png b/doc/images/workbench-dashboard.png
new file mode 100644
index 0000000..d8dec0e
Binary files /dev/null and b/doc/images/workbench-dashboard.png differ
diff --git a/doc/user/getting_started/workbench.html.textile.liquid b/doc/user/getting_started/workbench.html.textile.liquid
index 48a4c47..8140bba 100644
--- a/doc/user/getting_started/workbench.html.textile.liquid
+++ b/doc/user/getting_started/workbench.html.textile.liquid
@@ -10,4 +10,6 @@ Access the Arvados beta test instance available using this link:
If you are accessing Arvados for the first time, you will be asked to log in using a Google account. Arvados uses only your name and email address from Google services for identification, and will never access any personal information. Once you are logged in, the Workbench page may indicate your account status is *New / inactive*. If this is the case, contact the administrator of the Arvados instance to activate your account.
-Once your account is active, logging in to the Workbench will present you with a system status dashboard. This gives a summary of data, configuration, and activity in the Arvados instance.
+Once your account is active, logging in to the Workbench will present you with a system status dashboard. This gives a summary of data, configuration, and activity in the Arvados instance. The dashboard will display a welcome message if you have not yet created any projects. Create a new project by clicking on the <span class="btn-primary glyphicon-plus"> Add new project</span> button in the *My projects* panel in the dashboard.
+
+!{{ site.baseurl }}/images/workbench-dashboard.png!
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