Running bwa mem on AnVIL

I am trying out our WGS pipeline on AnVIL. I have uploaded a T/N pair and now want to run bwa mem. How do I create a cluster to run bwa? Should I create a conda environment to run bwa?

From Terra Support 2:32pm EDT

Your request (188047) has been received and is being reviewed by our support staff.

From Terra Support 4:32pm EDT

It looks like we are going to need more details, can you please share your workspace with by clicking the Share button in your workspace? The Share option is in the three-dots menu at the top-right.

  1. Add to the User email field and press enter on your keyboard .
  2. Click Save.

Please provide us with

  1. A link to your workspace

Also, when you say “create a cluster” are you referring to starting a cloud environment?

I don’t have permission to share my workspace.
Yes, I would like to run my WGS analysis on a cloud environment. I need some help setting it up.

From Terra Support 4:05pm EDT

No worries. Could you please share a link to where you found your workspace/ workflow so that I may reproduce it on my end?

In order to get started running workflows and doing analysis within Terra you will want to start a Cloud Environment by pressing the “Start cloud environment” button at the top right of your screen: ​

You may customize you Cloud Environment by pressing the cog to the right of the start environment button. From here you can customize you application configuration and the resources available to your Cloud Environment, unless specified otherwise in your workspace the default configurations should be sufficient.

Is there any other part of getting set up on Terra that I can help you with at this time? If you have any questions please feel free to let us know.