[ARVADOS] created: 1.1.4-714-g904e0b03f
Git user
git at public.curoverse.com
Thu Jul 26 14:32:42 EDT 2018
at 904e0b03fd558491d9dee39d7679a6c77eb6abd5 (commit)
commit 904e0b03fd558491d9dee39d7679a6c77eb6abd5
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Thu Jul 26 14:31:53 2018 -0400
13690: Walkthrough of Composer on Arvados
* Creating a new git repository through Arvados to store the workflow
* Creating CommandLineTools for “sort” and “uniq”
* Creating a Workflow which uses “sort” and “uniq” to remove duplicate lines from a text file
* Submitting the Workflow to run on Arvados
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
diff --git a/doc/_config.yml b/doc/_config.yml
index bad26fb18..03fc5af0c 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -24,6 +24,7 @@ navbar:
- Run a workflow using Workbench:
- user/getting_started/workbench.html.textile.liquid
- user/tutorials/tutorial-workflow-workbench.html.textile.liquid
+ - user/composer/composer.html.textile.liquid
- Access an Arvados virtual machine:
- user/getting_started/vm-login-with-webshell.html.textile.liquid
- user/getting_started/ssh-access-unix.html.textile.liquid
diff --git a/doc/css/images.css b/doc/css/images.css
index 0bd2ec7f0..73a1119f3 100644
--- a/doc/css/images.css
+++ b/doc/css/images.css
@@ -5,3 +5,11 @@ SPDX-License-Identifier: CC-BY-SA-3.0 */
img.full-width {
width: 100%
}
+
+img.screenshot {
+ max-width: calc(100% - 2em);
+ border: 3px;
+ border-style: solid;
+ margin-left: 2em;
+ margin-bottom: 2em;
+}
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diff --git a/doc/user/composer/composer.html.textile.liquid b/doc/user/composer/composer.html.textile.liquid
new file mode 100644
index 000000000..d6671013d
--- /dev/null
+++ b/doc/user/composer/composer.html.textile.liquid
@@ -0,0 +1,107 @@
+---
+layout: default
+navsection: userguide
+title: Create a Workflow with Composer
+...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+The Arvados Workflow Composer is a graphical interface for building Common Workflow Language (CWL) analysis workflows to run on Arvados.
+
+This tutorial will demonstrate:
+
+# Creating a new git repository through Arvados to store the workflow
+# Creating CommandLineTools for "sort" and "uniq"
+# Creating a Workflow which uses "sort" and "uniq" to remove duplicate lines from a text file
+# Submitting the Workflow to run on Arvados
+
+h3. 1. Access from workbench
+
+!(screenshot)c1.png!
+
+h3. 2. Composer starting page
+
+!(screenshot)c2.png!
+
+h3. 3. Manage git repositories (opens Workbench in new tab)
+
+!(screenshot)c2b.png!
+
+h3. 4. Add a new repository
+
+!(screenshot)c4.png!
+
+!(screenshot)c3.png!
+
+h3. 5. Return to Composer. Use refresh button to discover new repository (may take a few moments to show up).
+
+!(screenshot)c2c.png!
+
+h3. 6. Create a new Command Line Tool
+
+!(screenshot)c5.png!
+
+!(screenshot)c20.png!
+
+h3. 7. Set Docker image, base command, and input port for "sort" tool
+
+You may need to "upload a Docker image":{{site.baseurl}}/user/topics/arv-docker.html (@arv-keepdocker debian:8@)
+
+!(screenshot)c6.png!
+
+h3. 8. Redirect stdout to a file
+
+!(screenshot)c7.png!
+
+h3. 9. Capture output file
+
+!(screenshot)c8.png!
+
+h3. 10. Repeat steps 6-9 for "uniq" tool
+
+h3. 11. Create workflow
+
+!(screenshot)c9.png!
+
+!(screenshot)c10.png!
+
+h3. 12. Drag and drop tools into Workflow
+
+!(screenshot)c11.png!
+
+h3. 13. Drag and from input port of "sort" to empty space to create workflow input
+
+!(screenshot)c21.png!
+
+h3. 14. Drag from output port of "sort" to input port of "uniq"
+
+!(screenshot)c13.png!
+
+h3. 15. Drag and from output port of "uniq" to empty space to create workflow output
+
+!(screenshot)c14.png!
+
+h3. 16. Click on "Test" tab then click "Run"
+
+!(screenshot)c15.png!
+
+h3. 17. Choose input file
+
+You may need to "upload an input file":{{site.baseurl}}/user/tutorials/tutorial-keep.html
+
+!(screenshot)c16.png!
+
+h3. 18. Run the workflow
+
+!(screenshot)c17.png!
+
+h3. 19. Monitor progress
+
+!(screenshot)c18.png!
+
+h3. 20. Get workflow output
+
+!(screenshot)c19.png!
diff --git a/doc/user/topics/arv-docker.html.textile.liquid b/doc/user/topics/arv-docker.html.textile.liquid
index 1a78025b2..c21fbd9ad 100644
--- a/doc/user/topics/arv-docker.html.textile.liquid
+++ b/doc/user/topics/arv-docker.html.textile.liquid
@@ -184,14 +184,14 @@ arvados/jobs latest 12b9f859d48c 4 days ago
h2. Upload your image
-Finally, we are ready to upload the new Docker image to Arvados. Use @arv keep docker@ with the image repository name to upload the image. Without arguments, @arv keep docker@ will print out the list of Docker images in Arvados that are available to you.
+Finally, we are ready to upload the new Docker image to Arvados. Use @arv-keepdocker@ with the image repository name to upload the image. Without arguments, @arv-keepdocker@ will print out the list of Docker images in Arvados that are available to you.
<notextile>
-<pre><code>$ <span class="userinput">arv keep docker arvados/jobs-with-r</span>
+<pre><code>$ <span class="userinput">arv-keepdocker arvados/jobs-with-r</span>
703M / 703M 100.0%
Collection saved as 'Docker image arvados/jobs-with-r:latest 2818853ff9f9'
qr1hi-4zz18-abcdefghijklmno
-$ <span class="userinput">arv keep docker</span>
+$ <span class="userinput">arv-keepdocker</span>
REPOSITORY TAG IMAGE ID COLLECTION CREATED
arvados/jobs-with-r latest 2818853ff9f9 qr1hi-4zz18-abcdefghijklmno Tue Jan 17 20:35:53 2017
</code></pre>
@@ -207,9 +207,9 @@ hints:
h2. Share Docker images
-Docker images are subject to normal Arvados permissions. If wish to share your Docker image with others (or wish to share a pipeline template that uses your Docker image) you will need to use @arv keep docker@ with the @--project-uuid@ option to upload the image to a shared project.
+Docker images are subject to normal Arvados permissions. If wish to share your Docker image with others (or wish to share a pipeline template that uses your Docker image) you will need to use @arv-keepdocker@ with the @--project-uuid@ option to upload the image to a shared project.
<notextile>
-<pre><code>$ <span class="userinput">arv keep docker --project-uuid qr1hi-j7d0g-xxxxxxxxxxxxxxx arvados/jobs-with-r</span>
+<pre><code>$ <span class="userinput">arv-keepdocker --project-uuid qr1hi-j7d0g-xxxxxxxxxxxxxxx arvados/jobs-with-r</span>
</code></pre>
</notextile>
diff --git a/doc/user/tutorials/tutorial-workflow-workbench.html.textile.liquid b/doc/user/tutorials/tutorial-workflow-workbench.html.textile.liquid
index 6785ed68d..8dcb8e674 100644
--- a/doc/user/tutorials/tutorial-workflow-workbench.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-workflow-workbench.html.textile.liquid
@@ -19,6 +19,8 @@ A "workflow" (sometimes called a "pipeline" in other systems) is a sequence of s
h3. Steps
+notextile. <div class="spaced-out">
+
# 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.
# Click on the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a process...</span> button. This will open a dialog box titled *Choose a pipeline or workflow to run*.
# In the search box, type in *Tutorial bwa mem cwl*.
@@ -30,3 +32,5 @@ h3. Steps
# After the process starts running, you can track the progress by watching log messages from the component(s). This page refreshes automatically. You will see a <span class="label label-success">complete</span> label when the process completes successfully.
# Click on the *Output* link to see the results of the process. This will load a new page listing the output files from this process. 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>
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