[ARVADOS] updated: 35a3223ee35279c04552d5d3d372998711a956ab
git at public.curoverse.com
git at public.curoverse.com
Wed Aug 20 11:19:03 EDT 2014
Summary of changes:
doc/images/workbench-move-selected.png | Bin 0 -> 11267 bytes
.../getting_started/workbench.html.textile.liquid | 2 +-
doc/user/reference/api-tokens.html.textile.liquid | 8 +++---
...nning-pipeline-command-line.html.textile.liquid | 2 +-
doc/user/topics/tutorial-job1.html.textile.liquid | 4 +--
.../tutorial-firstscript.html.textile.liquid | 2 +-
.../tutorials/tutorial-keep.html.textile.liquid | 8 ++++--
...tutorial-pipeline-workbench.html.textile.liquid | 28 ++++++++++-----------
8 files changed, 29 insertions(+), 25 deletions(-)
create mode 100644 doc/images/workbench-move-selected.png
via 35a3223ee35279c04552d5d3d372998711a956ab (commit)
via 1a2947bd5c35d58a347111ad8a9f4fc50aa1d6b3 (commit)
via 57c56feabe58a4b49d0699c158086c13a5cdf023 (commit)
via 33755fab93fb604a5e663089ece0fe6d3f690fe4 (commit)
from de3b2f9a31e7d6df9fb53fff149f5ee43d1664d0 (commit)
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commit 35a3223ee35279c04552d5d3d372998711a956ab
Merge: de3b2f9 1a2947b
Author: Brett Smith <brett at curoverse.com>
Date: Wed Aug 20 11:18:54 2014 -0400
Merge branch '3499-home-project-docs-wip'
Closes #3516. Refs #3499.
commit 1a2947bd5c35d58a347111ad8a9f4fc50aa1d6b3
Author: Brett Smith <brett at curoverse.com>
Date: Fri Aug 15 16:08:52 2014 -0400
3499: Update Keep tutorial for recent UI changes.
diff --git a/doc/images/workbench-move-selected.png b/doc/images/workbench-move-selected.png
new file mode 100644
index 0000000..cae64d0
Binary files /dev/null and b/doc/images/workbench-move-selected.png differ
diff --git a/doc/user/tutorials/tutorial-keep.html.textile.liquid b/doc/user/tutorials/tutorial-keep.html.textile.liquid
index 59ebe84..74319fd 100644
--- a/doc/user/tutorials/tutorial-keep.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-keep.html.textile.liquid
@@ -28,9 +28,13 @@ c1bad4b39ca5a924e481008009d94e32+210
* The output value @c1bad4b39ca5a924e481008009d94e32+210@ is the Arvados collection locator that uniquely describes this file.
-Now go to the workbench collections page: <a href="https://{{ site.arvados_workbench_host }}/collections" target="_blank">https://{{ site.arvados_workbench_host }}/collections</a>. Your newly uploaded collection should appear near the top, with the value in the *uuid* column matching the Arvados collection locator that was printed by @arv-put at . Click on the *<i class="fa fa-fw fa-archive"></i> Show* button to go to the workbench page for your collection. Alternately, you can paste the Arvados collection locator into the *Search* box of the collections page to find your collection.
+Now visit the Workbench *Dashboard*. In the *My projects* pane, select your *Home* project. Your newly uploaded collection should appear near the top of the *Data collections* tab. The collection locator printed by @arv-put@ will appear under the *name* column. To move the collection to a different project, check the box at the left of the collection row. Pull down the *Selection...* menu near the top of the page tab, and select *Move selected*.
-The show collection page allows you to view the contents of the collection, download files from the collection, and set sharing options. To put your collection into a project, click on <span class="btn btn-xs btn-primary" ><i class="fa fa-fw fa-folder"></i> Add to project...</span>. This will open a modal dialog allowing you to select a destination project for your collection.
+!{{ site.baseurl }}/images/workbench-move-selected.png!
+
+This will open a dialog box where you can select a destination project for the collection. Click a project, then finally the <span class="btn btn-sm btn-primary">Move</span> button.
+
+Click on the *<i class="fa fa-fw fa-archive"></i> Show* button next to the collection's listing on a project page to go to the Workbench page for your collection. On this page, you can see the collection's contents, download individual files, and set sharing options.
notextile. </div>
commit 57c56feabe58a4b49d0699c158086c13a5cdf023
Author: Brett Smith <brett at curoverse.com>
Date: Fri Aug 15 15:38:04 2014 -0400
3499: Update pipeline tutorial for recent UI changes.
diff --git a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
index d0372b7..5df82a7 100644
--- a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
@@ -4,7 +4,7 @@ navsection: userguide
title: "Running a pipeline using Workbench"
...
-A "pipeline" (sometimes called a "workflow" in other systems) is sequence of steps that apply various programs or tools to transform input data to output data. Pipelines are the principal means of performing computation with Arvados. This tutorial demonstrates how to run a single-stage pipeline to take a small data set of paired-end reads from an sample "exome":https://en.wikipedia.org/wiki/Exome in "FASTQ":https://en.wikipedia.org/wiki/FASTQ_format format and align them to "Chromosome 19":https://en.wikipedia.org/wiki/Chromosome_19_%28human%29 using the "bwa mem":http://bio-bwa.sourceforge.net/ tool, producing a "Sequence Alignment/Map (SAM)":https://samtools.github.io/ file. This will introduce the following Arvados features:
+A "pipeline" (sometimes called a "workflow" in other systems) is a sequence of steps that apply various programs or tools to transform input data to output data. Pipelines are the principal means of performing computation with Arvados. This tutorial demonstrates how to run a single-stage pipeline to take a small data set of paired-end reads from a sample "exome":https://en.wikipedia.org/wiki/Exome in "FASTQ":https://en.wikipedia.org/wiki/FASTQ_format format and align them to "Chromosome 19":https://en.wikipedia.org/wiki/Chromosome_19_%28human%29 using the "bwa mem":http://bio-bwa.sourceforge.net/ tool, producing a "Sequence Alignment/Map (SAM)":https://samtools.github.io/ file. This will introduce the following Arvados features:
<div class="inside-list">
* How to create a project.
@@ -15,18 +15,18 @@ A "pipeline" (sometimes called a "workflow" in other systems) is sequence of ste
notextile. <div class="spaced-out">
-# Start from the *Workbench Dashboard*. You can return to the dashboard by clicking on *<i class="fa fa-lg fa-fw fa-home"></i> Home* in the upper left corner of any Workbench page.
-# Click on <span class="btn btn-sm btn-primary" > <i class="fa fa-fw fa-plus"></i> Add new project</span> on the "My projects" panel. This will direct you to the page for the new project.
-# On the new project page, click on the pencil icon <i class="fa fa-fw fa-pencil"></i> next to *New project* to pop up a text box and change the project title to *Tutorial output*. Click on <span class="btn btn-xs btn-primary" ><i class="glyphicon glyphicon-ok"></i></span> to save the new name.
-# Click on <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a pipeline...</span> This will open a modal dialog box titled *Choose a pipeline to run*.
-# Click on *<i class="fa fa-lg fa-fw fa-home"></i> Projects <span class="caret"></span>*. Under *Projects shared with me* select *<i class="fa fa-fw fa-share-alt"></i> Arvados Tutorial*.
-# Select *<i class="fa fa-fw fa-gear"></i> Tutorial align using bwa mem* and click on <span class="btn btn-sm btn-primary" >Next: choose inputs <i class="fa fa-fw fa-arrow-circle-right"></i></span>. This will load a new page where you will supply the inputs for the pipeline.
-# Click on <span class="btn btn-sm btn-primary" >Choose</span> under the first input parameter to the pipeline *reference_collection*. This will open a modal dialog box titled *Choose a dataset*.
-# Once again click on *<i class="fa fa-lg fa-fw fa-home"></i> Projects <span class="caret"></span>* and under *Projects shared with me* select *<i class="fa fa-fw fa-share-alt"></i> Arvados Tutorial*. Select *<i class="fa fa-fw fa-archive"></i> Tutorial chromosome 19 reference* and click on <span class="btn btn-sm btn-primary" >OK</span>.
-# Repeat the previous step to supply the *sample* parameter, this time choosing *<i class="fa fa-fw fa-archive"></i> Tutorial sample exome*.
-# Click on <span class="btn btn-sm btn-primary" >Run <i class="fa fa-fw fa-play"></i></span>.
-# This will refresh the page. The pipeline will be queued and shortly start running. You can track the progress by watching log messages from jobs. This page refreshes automatically. You will see <span class="label label-success">success</span> under the *job* the column when the pipeline completes successfully.
-# Click on *<i class="fa fa-fw fa-archive"></i> Show output files* to see the results of the job. This will load a new page listing the output files from this pipeline. Under the *Files* tab will be the output SAM file from the alignment tool
-# Click on the download icon <span class="btn btn-sm btn-info"><i class="fa fa-download"></i></span> to the right of the SAM file download your results.
+# Start from the *Workbench Dashboard*. You can access the Dashboard by clicking on *<i class="fa fa-lg fa-fw fa-dashboard"></i> Dashboard* in the upper left corner of any Workbench page.
+# In the *My projects* panel, click the <span class="btn btn-sm btn-primary" > <i class="fa fa-fw fa-plus"></i> Add new project</span> button. The new project will be created immediately, and your browser opens the new project's page for you to customize it.
+# On the new project page, click on the pencil icon <i class="fa fa-fw fa-pencil"></i> next to *New project* to pop up a text box and change the project title to *Tutorial output*. Click the <span class="btn btn-xs btn-primary" ><i class="glyphicon glyphicon-ok"></i></span> checkbox button to save the new name.
+# Click on the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a pipeline...</span> button. This will open a dialog box titled *Choose a pipeline to run*.
+# Click to open the *All projects <span class="caret"></span>* menu. Under the *Projects shared with me* header, select *<i class="fa fa-fw fa-share-alt"></i> Arvados Tutorial*.
+# Select *<i class="fa fa-fw fa-gear"></i> Tutorial align using bwa mem* and click the <span class="btn btn-sm btn-primary" >Next: choose inputs <i class="fa fa-fw fa-arrow-circle-right"></i></span> button. This will load a new page where you will supply the inputs for the pipeline.
+# The first input parameter to the pipeline is *Reference genoma (fasta)*. Click the <span class="btn btn-sm btn-primary">Choose</span> button beneath that header. This will open a dialog box titled *Choose a dataset for Reference genome (fasta)*.
+# Once again, open the *All projects <span class="caret"></span>* menu and select *<i class="fa fa-fw fa-share-alt"></i> Arvados Tutorial*. Select *<i class="fa fa-fw fa-archive"></i> Tutorial chromosome 19 reference* and click the <span class="btn btn-sm btn-primary" >OK</span> button.
+# Repeat the previous two steps to set the *Input genome (fastq)* parameter to *<i class="fa fa-fw fa-archive"></i> Tutorial sample exome*.
+# Click on the <span class="btn btn-sm btn-primary" >Run <i class="fa fa-fw fa-play"></i></span> button. The page updates to show you that the pipeline has been submitted to run on the Arvados cluster.
+# After the pipeline starts running, you can track the progress by watching log messages from jobs. This page refreshes automatically. You will see a <span class="label label-success">success</span> label under the *job* the column when the pipeline completes successfully.
+# Click on *<i class="fa fa-fw fa-archive"></i> Show output files* to see the results of the job. This will load a new page listing the output files from this pipeline. You'll see the output SAM file from the alignment tool under the *Files* tab.
+# Click on the <span class="btn btn-sm btn-info"><i class="fa fa-download"></i></span> download button to the right of the SAM file to download your results.
notextile. </div>
commit 33755fab93fb604a5e663089ece0fe6d3f690fe4
Author: Brett Smith <brett at curoverse.com>
Date: Fri Aug 15 11:44:46 2014 -0400
3499: Improve style consistency throughout docs.
* Capitalize Dashboard.
* Article use: "access Workbench," "access the Dashboard."
* Bold references to Workbench UI elements.
* Make example Arvados environment variables more realistic.
diff --git a/doc/user/getting_started/workbench.html.textile.liquid b/doc/user/getting_started/workbench.html.textile.liquid
index 02902b0..54ab71b 100644
--- a/doc/user/getting_started/workbench.html.textile.liquid
+++ b/doc/user/getting_started/workbench.html.textile.liquid
@@ -12,6 +12,6 @@ If you are using the default Arvados instance for this guide, you can Access Arv
You may 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. If you are accessing Arvados for the first time, the Workbench may indicate your account status is *New / inactive*. If this is the case, contact the administrator of the Arvados instance to request activation of your account.
-Once your account is active, logging in to the Workbench will present you with the *dashboard*. This gives a summary of your projects and recent activity in the Arvados instance. "You are now ready to run your first pipeline.":{{ site.baseurl }}/user/tutorials/tutorial-pipeline-workbench.html
+Once your account is active, logging in to the Workbench will present you with the Dashboard. This gives a summary of your projects and recent activity in the Arvados instance. "You are now ready to run your first pipeline.":{{ site.baseurl }}/user/tutorials/tutorial-pipeline-workbench.html
!{{ site.baseurl }}/images/workbench-dashboard.png!
diff --git a/doc/user/reference/api-tokens.html.textile.liquid b/doc/user/reference/api-tokens.html.textile.liquid
index 5cecd51..768c7d1 100644
--- a/doc/user/reference/api-tokens.html.textile.liquid
+++ b/doc/user/reference/api-tokens.html.textile.liquid
@@ -10,16 +10,16 @@ Access the Arvados Workbench using this link: "https://{{ site.arvados_workbench
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).
-Click on the link with your _email address_ in the upper right corner 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 the *Current Token* panel, which lists your current token and instructions to setup your environment.
+Click on the link with your _email address_ in the upper right corner to access your account menu, then click on the menu item *Manage account* to go to the account management page. On the *Manage account* page, you will see the *Current Token* panel, which lists your current token and instructions to set up your environment.
-h2. Setting the environment
+h2. Setting environment variables
-For your convenience, the "Manage account" page on Workbench provides the "Current Token" panel that includes a command you may copy and paste directly into the shell. It will look something as the following.
+For your convenience, the *Manage account* page on Workbench provides the *Current Token* panel that includes a command you may copy and paste directly into the shell. It will look something as the following.
bc. HISTIGNORE=$HISTIGNORE:'export ARVADOS_API_TOKEN=*'
export ARVADOS_API_TOKEN=2jv9346o396exampledonotuseexampledonotuseexes7j1ld
export ARVADOS_API_HOST={{ site.arvados_api_host }}
-export ARVADOS_API_HOST_INSECURE=true
+unset ARVADOS_API_HOST_INSECURE
* The @export@ command puts a local shell variable into the environment that will be inherited by child processes such as the @arv@ client.
diff --git a/doc/user/topics/running-pipeline-command-line.html.textile.liquid b/doc/user/topics/running-pipeline-command-line.html.textile.liquid
index c295842..85d9188 100644
--- a/doc/user/topics/running-pipeline-command-line.html.textile.liquid
+++ b/doc/user/topics/running-pipeline-command-line.html.textile.liquid
@@ -30,7 +30,7 @@ bwa-mem qr1hi-8i9sb-67n1qvsronmd2z6 49bae1066f4ebce72e2587a3efa61c7d+88
</code></pre>
</notextile>
-This instantiates your pipeline and displays a live feed of its status. The new pipeline instance will also show up on Workbench dashboard.
+This instantiates your pipeline and displays a live feed of its status. The new pipeline instance will also show up on the Workbench Dashboard.
Arvados adds each pipeline component to the job queue as its dependencies are satisfied (or immediately if it has no dependencies) and finishes when all components are completed or failed and there is no more work left to do.
diff --git a/doc/user/topics/tutorial-job1.html.textile.liquid b/doc/user/topics/tutorial-job1.html.textile.liquid
index d2fb309..e231c9b 100644
--- a/doc/user/topics/tutorial-job1.html.textile.liquid
+++ b/doc/user/topics/tutorial-job1.html.textile.liquid
@@ -88,11 +88,11 @@ The job is now queued and will start running as soon as it reaches the front of
h2. Monitor job progress
-Go to "*Recent jobs*":https://{{site.arvados_workbench_host}}/jobs in the Workbench. Your job should be near the top of the table. This table refreshes automatically. When the job has completed successfully, it will show <span class="label label-success">finished</span> in the *Status* column.
+Go to "*Recent jobs*":https://{{site.arvados_workbench_host}}/jobs in Workbench. Your job should be near the top of the table. This table refreshes automatically. When the job has completed successfully, it will show <span class="label label-success">finished</span> in the *Status* column.
h2. Inspect the job output
-On the "Workbench dashboard":https://{{site.arvados_workbench_host}}, look for the *Output* column of the *Recent jobs* table. Click on the link under *Output* for your job to go to the files page with the job output. The files page lists all the files that were output by the job. Click on the link under the *file* column to view a file, or click on the download icon <span class="glyphicon glyphicon-download-alt"></span> to download the output file.
+On the "Workbench Dashboard":https://{{site.arvados_workbench_host}}, look for the *Output* column of the *Recent jobs* table. Click on the link under *Output* for your job to go to the files page with the job output. The files page lists all the files that were output by the job. Click on the link under the *file* column to view a file, or click on the download button <span class="glyphicon glyphicon-download-alt"></span> to download the output file.
On the command line, you can use @arv job get@ to access a JSON object describing the output:
diff --git a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
index b045d62..d59275d 100644
--- a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
@@ -98,4 +98,4 @@ Although the job runs locally, the output of the job has been saved to Keep, the
</code></pre>
</notextile>
-Running locally is convenient for development and debugging, as it permits a fast iterative development cycle. Your job run is also recorded by Arvados, and will show up in the "Recent jobs and pipelines" panel on the "Workbench dashboard":https://{{site.arvados_workbench_host}}. This provides limited provenance, by recording the input parameters, the execution log, and the output. However, running locally does not allow you to scale out to multiple nodes, and does not store the complete system snapshot required to achieve reproducibility; to that you need to "submit a job to the Arvados cluster":{{site.baseurl}}/user/tutorials/tutorial-submit-job.html
+Running locally is convenient for development and debugging, as it permits a fast iterative development cycle. Your job run is also recorded by Arvados, and will appear in the *Recent jobs and pipelines* panel on the "Workbench Dashboard":https://{{site.arvados_workbench_host}}. This provides limited provenance, by recording the input parameters, the execution log, and the output. However, running locally does not allow you to scale out to multiple nodes, and does not store the complete system snapshot required to achieve reproducibility; to do that you need to "submit a job to the Arvados cluster":{{site.baseurl}}/user/tutorials/tutorial-submit-job.html.
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