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bids-apps / MRtrix3_connectome

Generate subject connectomes from raw BIDS data & perform inter-subject connection density normalisation, using the MRtrix3 software package.
http://www.mrtrix.org/
Apache License 2.0
49 stars 26 forks source link

Dockerhub is behind by 6 months #38

Closed dkp closed 5 years ago

dkp commented 5 years ago

It would be great if dockerhub build was updated.

Lestropie commented 5 years ago

The Dockerhub container is 6 months old because the App hasn't really been updated in 6 months :-/ I have a series of changes occurring in the main MRtrix3 repository that will eventually need to be reflected in this App, but I've not been able to commit time to this App of late. Hopefully when I get back to completing the manuscript for this App I can add some outstanding things.

Regarding the original post:

Step 7/56 : RUN apt-key adv --recv-keys --keyserver pgp.mit.edu 2649A5A9
---> Running in e363055aeefa
Executing: /tmp/apt-key-gpghome.nB2rGV2iyT/gpg.1.sh --recv-keys --keyserver pgp.mit.edu 2649A5A9
gpg: keyserver receive failed: No data
The command '/bin/sh -c apt-key adv --recv-keys --keyserver pgp.mit.edu 2649A5A9' returned a non-zero code: 2

This unfortunately occurs sporadically, and is usally solved by just re-running the build. I saw a trick in another repository where they store the required key data in a file within the repository and import it into the container during the build process; I will likely use the same technique in the future.

dkp commented 5 years ago

Hmm, as far as I can tell, the last dockerhub build reports being a year old, not 6 months old. The dockerfile available for viewing on dockerhub uses ubuntu 14.04. However, the dockerfile here: https://github.com/BIDS-Apps/MRtrix3_connectome/blob/master/Dockerfile is using ubuntu 18.

Lestropie commented 5 years ago

I'm not quite sure what's going on there. Both 0.3.0 and latest show as being 7 months old for me. But DockerHub doesn't seem to offer a great deal of control (at least from my account). I'll have a close look after pushing 0.4.0.

Lestropie commented 5 years ago

@dkp: Version 0.4.0 is now up on DockerHub. Changes described in #40.

It seems however that the Dockerfile showing on the DockerHub website is still out of date, i.e. is from an older version of the App, and I don't appear to have any control over that from within my DockerHub account. @chrisfilo: Have you encountered this previously? Any idea why the Dockerfile shown on the DockerHub website would not track the :latest tag?

dkp commented 5 years ago

I've pulled the image now and it updated a BUNCH of layers...(though I see a bunch of "failed" messages on dockerhub). I've just told it to run with --debug mode on, and with --output_verbosity 3 but I am not sure what it is doing...I see no temp directory nor any output at the command line.

I tried running with --version and it did not return any info to the command line. So maybe the dockerhub builds really did fail.

I'm new to this stuff, so my experiences are those of a novice. Nevertheless, here are the problems I've dealt with getting dockerhub to behave :

1) I've had problems with the webhooks getting broken or corrupted (after I fooled around renaming and recreating the git repository on line). 2) AND I've had problems with the whole automated system producing corrupted builds of my project. I had more success with manual builds like this: push to the hub:

docker login (enter credentials) docker tag bipbids diannepat/bipbids docker push diannepat/bipbids