day one firecloud newbiequestion ... can't pull docker image

[email protected]

I type in linux command line: docker pull broadinstitute/cromwell
I see ...
Using default tag: latest
Pulling repository docker.io/broadinstitute/cromwell
Tag latest not found in repository docker.io/broadinstitute/cromwell

Any easy solutions?

jneff

Hi Richard,

Cromwell is FireCloud's execution service for WDL workflows. Apparently, Cromwell (the Lord Protector) was known for executing kings, hence the name. It is open-source project that you can download from Github, although it would not be particularly helpful for accessing TCGA BAM files.

You can find small BAMs from the open access BroadMutationCalling workspace. Assuming you are now activated, try typing BroadMutationCalling into the workspace search bar. Then, in that workspace's Data tab, under the sample view, you can click on and download BAMs.

Another option would be to view the controlled access workspaces within FireCloud. You would need to have dbGaP authorization and link your eRA Commons account. Instructions here.

Let us know if you have any other questions!

Jason

jneff

Hi Richard,

Are you trying to install Cromwell locally?

Jason

[email protected]

I want to download a template docker image (one that hopefully gives me a clue on how to access a TCGA bam file , access this file, produce output and fetch ithe output).
I just figured I'd pick a random one to see what the Lord Protector is all about, see if he's got a good starting template.

jneff

Hi Richard,

Cromwell is FireCloud's execution service for WDL workflows. Apparently, Cromwell (the Lord Protector) was known for executing kings, hence the name. It is open-source project that you can download from Github, although it would not be particularly helpful for accessing TCGA BAM files.

You can find small BAMs from the open access BroadMutationCalling workspace. Assuming you are now activated, try typing BroadMutationCalling into the workspace search bar. Then, in that workspace's Data tab, under the sample view, you can click on and download BAMs.

Another option would be to view the controlled access workspaces within FireCloud. You would need to have dbGaP authorization and link your eRA Commons account. Instructions here.

Let us know if you have any other questions!

Jason

[email protected]

Is there a docker image for this "BroadMutationCalling" I can pull? I'm really interested in accessing the TCGA bam files and if that image can access the bams then I can probably figure out how to do things.

jneff

Hi Richard,

A Docker image contains a tool for FireCloud. The FireCloud platform is responsible for gathering workflow and task inputs from the data model and method configuration, and passes them into the tool at run time. In other words, the tool itself is NOT responsible for accessing the BAM files, this is done by the FireCloud Platform. So pulling a docker image containing a tool, or a WDL representation of a workflow will not provide you with any insight into how BAM files are accessed.

Maybe it would be helpful if we could arrange a time to chat on the phone about this?

Thanks