Setting up Dockstore app with existing workflows

Dockstore
1

Hi,
I’d like to setup the automatic syncing with the Dockstore Git app. After reading the documentation we’ve

  1. Enabled the Dockstore App Git plugin in the git repo
  2. Added a yml file to the repo.

However, after pushing a new branch to the repo i don’t see the branch populate for the associated workflow in Dockstore. Are there any additional tasks that needs to be done? I’ve noticed the Mode for the gatk repo workflows are still set to is set to FULL. Are they suppose to be DOCKSTORE_YML?

Screen Shot 2020-10-21 at 10.30.30
Screen Shot 2020-10-21 at 10.30.30376×379 19.1 KB

2

Hello,

Your .dockstore.yml is missing the version field. You need something like:

version: 1.2
workflows:
   - name: cnv_germline_case_workflow
     subclass: WDL
     primaryDescriptorPath: /scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl
     ...

You should be able to see any GitHub apps log activity by clicking on the “See GitHub Apps Logs” button for your GitHub organization on the Dockstore My Workflows page. That should be surfacing the error you are running into – let’s us know if you don’t see it. Here’s my view for one of my orgs:

Screen Shot 2020-10-21 at 11.32.03 AM
Screen Shot 2020-10-21 at 11.32.03 AM590×359 17.1 KB

3

Thanks,
Prior to adding the version line in the yml many of the GitHub Apps logs looked like thisScreen Shot 2020-10-21 at 15.55.01
Like you said the yml file is not valid
I recently created a pr to fix the file, and the push for this pr created the following log
Screen Shot 2020-10-21 at 15.55.14
Hopefully it just needs some time to sync with Github, I’ll keep in contact if something is amiss.

4

Hi,

We’re looking into this. Could you please try another push on the branch that has the .dockstore.yml?

Thanks,

Charles

5

As further followup, I see the error twice in our logs. One of them is a known problem, https://github.com/dockstore/dockstore/issues/3689 – we expect to release a fix for that today.

The other one I’m not sure what is going on.

In cloning the broadinstitute/gatk repo to look at this, I see that the repo uses Git Large File Storage. Do you know if that’s been the case for a while, or is that relatively recent? I don’t think it should matter, but just want to check if that’s a recent change.

Charles

6

Thanks for the update. Yes, gatk has used git LFS almost since the beginning of the gatk4 repo

7

Hi Charles,

I tried again today and recieved the same message from the Git logs:

2020-10-23T08:46 bshifaw gatk refs/heads/bs_dockstore_test Failed Push
Could not reach GitHub, please try again later