Arvados

h1. Running Tuxedo tools (Bowtie > Tophat > Cufflinks) using Arvados

This tutorial demonstrates how to tests for differential expression and regulation in RNA-Seq samples using Cufflinks. The RNA-Seq pipeline consisting of "Bowtie 2":http://bowtie-bio.sourceforge.net/bowtie2/index.shtml, "Tophat 2":http://ccb.jhu.edu/software/tophat/index.shtml, and "Cufflinks":http://cole-trapnell-lab.github.io/cufflinks/. This tutorial introduces the following Arvados features:

* How to run the Tuxedo Suite Pipeline using Arvados

* How to access your pipeline results.

* How to browse and select your input data for the Tuxedo Suite Pipeline and submit re-run the pipeline.

# Start at the "Curoverse":https://curoverse.com/ website and click Log In at the top. We currently support all Google / Google Apps accounts for authentication. By simply choosing a Google-based account, your account will be automatically created and redirect to the "Arvados Workbench":https://workbench.qr1hi.arvadosapi.com/.

# In the *Active pipelines* panel, click on the *Run a pipeline...* button. Doing so opens a dialog box titled *Choose a pipeline to run*.

# Select *Tuxedo Suite Pipeline (public)* and click the *Next: choose inputs* button. Doing so loads a new page to supply the inputs for the pipeline.

# The default inputs from the Tuxedo Suite Pipeline source code repository are already pre-loaded. Click on the *Run* 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 its progress by watching log messages from jobs.  This page refreshes automatically.  You will see a complete label under the job the column when the pipeline completes successfully. The current run time of the job in CPU and clock hours is also displayed. You can view individual job details by clicking on the job name.

# Once the job is finished, the output can be viewed to the right of the run time.

# Click on the download button to the right of the file to download your results, or the magnifying glass to quickly view your results.

h2. Uploading data through the web and using it on Arvados

WIP

h2. Uploading data through your shell and using it on Arvados

WIP

h3. FAQ

WIP