Running bcbio-nextgen using Arvados¶

WIP

Uploading data through the web and using it on Arvados¶

1. In your home project, click on the blue + Add data button in the top right.
2. Click Upload files from my computer
3. Click Choose Files and choose the 2 paired end fastq files you would like to run bcbio-nextgen on.
4. Once you're ready, click > Start
5. 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
6. Once that is uploaded, navigate back to the dashboard and click on Run a pipeline... and choose bcbio-nextgen pipeline.
7. You can change the input by clicking on the [Choose] button next to the R1 parameter and R2 parameter.
8. Input your left fastq file as R1 and your right fastq file as R2.
9. For each fastq file, click on the dropdown menu, click on your newly-created project, and choose your desired input collection.
10. Click Run to run bcbio on your data!

Uploading data through your shell and using it on Arvados¶

WIP

FAQ¶

WIP