17245: documentation: remove unlinked pages.

[arvados.git] / doc / user / composer / composer.html.textile.liquid

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----
-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) 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
-
-The "Docker Repository" is the name:tag of a "Docker image uploaded Arvados.":{{site.baseurl}}/user/topics/arv-docker.html (Use @arv-keepdocker --pull debian:8@)  You can also find prepackaged bioinformatics tools on various sites, such as http://dockstore.org and http://biocontainers.pro/ .
-
-!(screenshot)c6.png!
-
-h3. 8. Redirect stdout to a file
-
-!(screenshot)c7.png!
-
-h3. 9. Capture output file
-
-!(screenshot)c8.png!
-
-h3. 10. Save Command Line Tool
-
-!(screenshot)c22.png!
-
-h3. 11. Repeat steps 6-10 for "uniq" tool
-
-Create a new tool with a "base command" of "uniq".
-
-h3. 12. Switch back to "Home" tab and create workflow
-
-!(screenshot)c24.png!
-
-!(screenshot)c9.png!
-
-!(screenshot)c10.png!
-
-h3. 13. Drag and drop tools into Workflow
-
-!(screenshot)c11.png!
-
-h3. 14. Drag from input port of "sort" to empty space to create workflow input
-
-!(screenshot)c21.png!
-
-h3. 15. Drag from output port of "sort" to input port of "uniq"
-
-!(screenshot)c13.png!
-
-h3. 16. Drag from output port of "uniq" to empty space to create workflow output
-
-!(screenshot)c14.png!
-
-h3. 17. Save Workflow
-
-!(screenshot)c23.png!
-
-h3. 18. Click on "Test" tab then click "Run"
-
-!(screenshot)c15.png!
-
-h3. 19. Choose input file
-
-You may need to "upload an input file":{{site.baseurl}}/user/tutorials/tutorial-keep.html
-
-!(screenshot)c16.png!
-
-h3. 20. Run the workflow
-
-!(screenshot)c17.png!
-
-h3. 21. Monitor progress (may take several minutes)
-
-!(screenshot)c18.png!
-
-h3. 22. Get workflow output
-
-!(screenshot)c19.png!