Docker internal error

Posted in Add your tools by Franco Caramia Wed Jun 22 2016 04:46:26 GMT+0000 (UTC)·8·Viewed 813 times

Hi there, I'm trying to run a tool I developed. I committed the docker container and tested the execution of the tool locally. I get the following error when running my tool: "Error This task ran into a problem during execution and did not finish. Failed to start exmut. Internal error: Docker container failed to start." Is there anyway I can debug this? Thanks
Anjan Purkayastha
June 22, 2016

I am getting a similar comment with my docker image.
Some help from SBG developers will definitely be appreciated.
-Anjan

Gaurav Kaushik
June 22, 2016

Hi Franco and Anjan,

There are a few options for debugging a task where the Docker container seems to have failed to start.

  1. Try rerunning the task once more. Sometimes pulls from DockerHub can fail or there can be an issue with the computing instance. This is the best first option if your tool has worked previously.

  2. Confirm that you pushed the container to a registry. To push to the CGC image registry, you must login into the CGC using your username and authentication token (as the password). To push, enter docker push cgc-images.sbgenomics.com/<cgc-username>/<project-name>:<tag>. To push to DockerHub, docker push <dockerhub-username>/<container>:<tag>.

If you pushed the container successfully, you should be able to pull it. Try using the docker pull command to do that. Docker will check for any updates and report "Status: Image is up to date for <image>".

  1. Confirm that you used that exact image URL in the Tool Editor to call your tool. Be sure to add the tag as well (even if you're using the 'latest' image).

Here is a link to all of our documentation on pushing Docker images for use on the CGC: http://docs.cancergenomicscloud.org/docs/upload-your-docker-image

Franco Caramia
June 23, 2016

Hey Gaurav,

Many thanks for your help again.

I had forgotten to push my image. But now I got an authorisation problem when trying to push:

$ docker push cgc-images.sbgenomics.com/xxxxxx/xxxxx:v1
The push refers to a repository [cgc-images.sbgenomics.com/xxxxxx/xxxxx]
dfd3e1e747f5: Preparing
5f70bf18a086: Preparing
737f40e80b7f: Preparing
82b57dbc5385: Preparing
19429b698a22: Preparing
9436069b92a3: Waiting
unauthorized: authentication required

I've searched a bit and appears to be a known problem with the docker jason credentials.

My jason file looks like this:

$ cat ~/.docker/config.json
{
"auths": {
"cgc-images.sbgenomics.com": {
"auth": "xxxxxxxxxxxxxxx"
}
}
}

Some people solved the issue by adding "email" to the jason file, this did not work for me.

Do you have any suggestions?

Thanks!

Franco Caramia
June 23, 2016

Hi Gaurav,

In addition, I noticed that my cgc URL is :

https://cgc.sbgenomics.com/u/LASTNAME/project/ where LASTNAME is all in uppercase.

When I check my tool, the json file contains:
"sbg:id": "LASTNAME/project/toolname/10" where LASTNAME is all in uppercase.

When I try to commit and push my docker container, I'm only allowed to use lowercase for the tag. So: "cgc-images.sbgenomics.com/lastname/toolname:v1", where lastname is all lowercase

Wondering if this got anything to do with the issue.

Thanks,

Franco Caramia
June 23, 2016

I was able to push my image to docker.io.

I set the URL to point to my docker.io repo in my tool editor. I'm trying to run the tool but now my CGC GUI is not loading....When clicking in Tasks I get "There was an error"

Anjan Purkayastha
June 23, 2016

All,
Thanks for this helpful discussion. Eric was kind enough to look into my problem. I created a fresh image of my application and pushed it into cgc.sbgenomics.com. Most importantly, when specifying the docker image, within my CGC app, I appended the "latest" tag. Once that was added- the image worked as expected.
HTH,
Anjan

Franco Caramia
June 23, 2016

Thanks for the info Anjan. I changed the url of my config.json to "https://cgc-images.sbgenomics.com" and the image is now pushing.

I'll try your tag, thanks!

Gaurav Kaushik
June 23, 2016

Hi Anjan and Franco,

Thanks for updating everyone here! I think this will be helpful for other users.

Seems like images are pushing OK. If any other Docker issues arise, please update :)

  
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