latest tag not available for certain containers built from mulled about containers HOT 13 CLOSED

Thans @iSnow for using BioContainers. The point for searching a container in the web is: http://biocontainers.pro/registry/#/, there you can search for the corresponding container. For example a search there will give you the openbabel container
(http://biocontainers.pro/registry/#/showImages?domain=quay&repository=openbabel&starred=false&modified=05%2F11%2F2016).

We will update the documentation here biocontainers.pro/docs but feel free to suggest and contribute to it. We are now discussing how to add a default tag to each mulled container.

from containers.

@bgruening do you know why the quay.io containers do not have the latest version?

from containers.

We simply did not implement it. In theory this should be easy we could simply link "some" container to the :latest version. The tricky question is how to determine what is the latest version. Depending on the version schema this can be tricky. But the most important part is at which time point to we want to create this link? On the bioconda side - when a new container is pushed? As a separate service?

Is this an important feature to have? Can we not solve this with tooling? For example mulled-search returns an entire command which you can use, including the correct version.

from containers.

ok. I think the main point is that we need to make clear in the interface of the registry UI which is the version because right now is building the docker command taking into account that latest exists.

from containers.

Yes, my point was more towards what @ypriverol wrote, if the UI advertises a pull command, then it should work out of copy pasting the command. If you don't want to have a latest, then the (registry) UI should point to a version in the pull command, that's all.

Whether to have a latest or not, I guess it is a separate discussion. My quick thought on this would be that not having a latest might not be a good idea considering that people used to docker containers probably expect to find it. And then, using a version on the UI's pull command is more or less analogous to choosing a latest, you're still "blessing" a version. Question is whether the UI or the container maintainer should decide this, probably the latter in my opinion.

from containers.

Question is whether the UI or the container maintainer should decide this, probably the latter in my opinion.

There is no container maintainer anymore, this needs to happen completely automatically and this is where I'm a little bit afraid. I think the quick way is to fix the UI and if someone has time we could implement a mechanism to update the latest version somehow. I know that the quay.io API supports this - I just don't have time the next month I think :(

from containers.

Yes, I understand where you come from. Do you have different branches or channels for the containers? such as master and develop? or stable and bleeding edge? Maybe every time that the master/stable is built, that container could be blessed as latest.

from containers.

Oh no, I have a bioconda package and as soon as this is available I create a container for it :)
Problem is that you can add Conda package for old software, what we did to migrate a lot of Galaxy tools to Conda ... this means the latest Conda package that was build for tool X does not mean it should be latest.

from containers.

Ok @bgruening but can we add this tag to the bioconda recipe and then used during the creating of the container?

from containers.

Wich tag? If you add latest to all recipes, all will end up as latest :)

from containers.

So, how do I go about pulling and starting a biocontainers docker image? And pardon my ignorance, what is mulled-search? Looking for it at Google leads me to a lot of wine sites, but no software.

I am specifically looking at running the openbabel container from quay.io, would it be possible to attach a bit more information, like how to pull any recent image? Or does it include a REST service and on which port does it run or do you link in a path like in the BLAST example?

Biocontainers seems like a very nice and useful project, however a bit developer-centric right now. So, adding some end-user information would be awesome :)

Thanks for all your work!

from containers.

@bgruening and @pcm32 I have been thinking about adding the specific tag to the UI now but, for best practices, I think it will be good to have the latest version of each mulled container. If I try to do that in the UI it will be also a guessing process. Then I really think we should do this systematically. How we can implement this @bgruening

from containers.

@iSnow I have added a more obvious statement how you can install the utilities in https://github.com/BioContainers/edu/blob/master/series/faqs/galaxy_container_dependencies.md

Essentially, mulled-search and all the other tooling is currently part of galaxy-lib:

pip install galaxy-lib

@ypriverol the problem is that it is not easy to guess the most recent version, because naming schema are not standardized. So we will make mistakes.

from containers.