Arvados

h1. Running bcbio-nextgen using Arvados

WIP

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 the 2 paired end fastq files you would like to run bcbio-nextgen 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 bcbio-nextgen pipeline.

# You can change the input by clicking on the *[Choose]* button next to the *R1 parameter* and *R2 parameter*.

# Input your left fastq file as R1 and your right fastq file as R2.

# For each fastq file, click on the dropdown menu, click on your newly-created project, and choose your desired input collection. 

# Click *Run* to run bc-bio on your data!

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

WIP

h3. FAQ

WIP