Arvados

h1. Running GATK2 using Arvados

This tutorial demonstrates how to run the GATK Unified Genotyper pipeline using GenomeAnalysisTK-2.2-16 from the Broad Institute.

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

# In your home project, click on the blue *+ Add data* button in the top right.

# Click *Upload files from my computer*

# Click *Choose Files* and choose one set of paired end fastq files you would like to run GATK2 on.

# Once you're ready, click *> Start*

# Feel free to rename your Collection so you can remember it later. Click on the pencil icon in the top left corner next to *New collection*

# Once that is uploaded, navigate back to the dashboard and click on *Run a pipeline...* and choose GATK2 / exome PE fastq to snp [dev] [public].

# You can change the input by clicking on the *[Choose]* button next to the *Sample FASTQ reads*.

# Click on the dropdown menu, click on your newly-created project, and choose your desired input collection. Click *OK* and *Run* to run lobSTR v.3 on your data!

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

Full documentation can be found "here":http://doc.arvados.org/user/tutorials/tutorial-keep.html

# Install the "Arvados Python SDK":http://doc.arvados.org/sdk/python/sdk-python.html on the system from which you will upload the data (such as your workstation, or a server containing data from your sequencer). Doing so will install the Arvados file upload tool, arv-put.

# To configure the environment with the Arvados instance host name and authentication token, see "here":http://doc.arvados.org/user/reference/api-tokens.html 

# Navigate back to your Workbench dashboard and create a new project by clicking on the Projects dropdown menu and clicking Home. 

# Click on [+ Add a subproject]. Feel free to edit the Project name or description by clicking the pencil to the right of the text.

# To add data, return to your shell, create a folder, and put the two paired-end fastq files you want to upload inside. Use the command arv-put * --project-uuid qr1hi-xxxxx-yyyyyyyyyyyyyyy. The qr1hi tag can be found in the url of your new project. This ensures that all the files you would like to upload are in one collection.

# The output value xxxxxxxxxxxxxxxxxxxx+yyyy is the Arvados collection locator that uniquely describes this file.

# Once that is uploaded, navigate back to the dashboard and click on *Run a pipeline...* and choose GATK2 / exome PE fastq to snp [dev] [public].

# You can change the input by clicking on [Choose] next to the *Sample FASTQ reads*.

# Click on the dropdown menu, click on your newly-created project, and choose your desired input collection. Click *OK* and *Run* to run GATK2 on your data!

h3. FAQ

WIP