biocontainers / mulled Goto Github PK

Accept 1.0.0 as well as 1.0.0--7

see #17

For example this link does not work:
https://travis.ci.org/mulled/mulled.github.io/builds/115003733/

I guess it is ok to remove it.

Singularity was brought up by @moskalenko.

Comparison of the two. https://groups.google.com/a/lbl.gov/forum/m/#!topic/singularity/-dl2i8vkGf8

All that would need to be done is an export from the built docker image to a singularity image. Shouldn't be too hard. :)

Is there a way to do this automatically from a Galaxy tool - I'm not seeing that. I thought that was the goal? Is that something I can help with - I'd like to use galaxy-lib for parsing and finding tool XML files - the abstractions will mean other tool format such as CWL will work automatically then also.

If we include a samtools and a conda "samtools" package we need to decide how to handle this collision.
We could also block every PR that tries to add a namespace conflict for the beginning. Like create Image name out of metadata, check if it's already there, don't merge and provide a meaningful error message in travis.

If a package is removed from packages.tsv, it should be removed from Quay.io as well. However, the exact semantics are not that obvious.

• Should all tags that have no equivalent in packages.tsv be removed?
• Or only whole repositories that do not occur anymore?

All Biocontainers ship with implementations of basic tools based on non-GNU implementations (BusyBox from 2014). Tools such as sleep, date, ls in these containers do not accept standard arguments and options, breaking pipelines for which Biocontainers could in principle be used as a 1:1 replacement for existing tools. In practice, these non-GNU tools break existing pipelines to an extent that discourages adoption of Biocontainers. For an example, see here:

nextflow-io/nextflow#321

This is one example of many. Would it be possible to ship Biocontainers with a more modern, still lightweight base image?

I can't access https://quay.io/mulled/samtools only mulled_dev

docker run -it quay.io/mulled/samtools:1.3--1
Unable to find image 'quay.io/mulled/samtools:1.3--1' locally
Pulling repository quay.io/mulled/samtools
docker: Error: Status 403 trying to pull repository mulled/samtools: "{\"error\": \"Permission Denied (user: leipzig)\"}".

It would be nice to build all versions of a package given the version number *, at least for package managers that support it.

Moreover, if we do not consider the build string in conda, we need a way to trigger a rebuild.
What do you think?

Hi,

the biocontainer community is asking to move this repository under the biocontainers namespace. This is ok for me, but I think it will break the website or will need some work after the migration. Moreover, the biocontainer guys have there own website presenting containers from quay.io (http://biocontainers.pro/registry/).

So do we want to keep this website? Do we want to move the repo?
ping @erasche @thriqon

Hello all,

Since it was announced biocontainers are mirrored on ECR https://gallery.ecr.aws/biocontainers, I was wondering what steps would need to happen to get the mulled containers mirrored there as well?

The image can be pushed but the metadata times out to be pushed.

https://travis-ci.org/mulled/mulled/jobs/151961283