It’s still in beta
Some news on a container standard -http://techcrunch.com/2015/06/22/docker-coreos-google-microsoft-amazon-and-others-agree-to-develop-common-container-standard/
A container runtime too - http://blog.docker.com/2015/06/runc
Open containers project - https://www.opencontainers.org/
biobox short-read-assemble bioboxes/velvet -i FASTQ -o CONTIGS
I think the syntax is clear and just what I was thinking of. I'd suggest to make it a bit more abstract for further extension and then simplify via shortcuts/alias names like:
biobox run --container docker://bioboxes/velvet --specification biobox.yaml --arguments -i FASTQ -o CONTIGS
or shorthand:
biobox run docker://bioboxes/velvet -i FASTQ -o CONTIGSdocker:// is the container runtime backend
run is analogous to docker run (further commands to be added),
the specification can be passed as a file but if the biobox command can link the container id and the spec itself via metadata, then there is no need to pass it.
IMO, there should also be an option to pass the YAML file itself (I believe it is better to let the YAML file point to valid data on the local system and to let the biobox wrapper transform it to paths according to the container-internal mount points before passing it to the containe)
just my two cents...
this is some module which can create a python argparse (option parsing) object directly from a YAML or JSON file: https://github.com/fmenabe/python-clg
it might be useful
it might be useful
Sounds like Peter’s talk at BOSC went well - https://twitter.com/GigaScience/status/619823935933284352
Definitely the right place to present bioboxes
This allows the following command
biobox short_read_assembler bioboxes/megahit --verify
This verifies that a short_read_assembler biobox conforms to the spec.
I’m most excited about this because building and testing new biobox docker containers is not easy, but this makes it much more so.
I may be late in finding out about this DinD approach but here it goes: https://twitter.com/ProfParmer/status/651835246158024704
NERSC have created ‘shifter’ which seems to provide a safer way to do this in a HPC environment - https://www.nersc.gov/news-publications/nersc-news/nersc-center-news/2015/shifter-makes-container-based-hpc-a-breeze/
Hi there, at the moment I see very few bioboxes available and their presentation as a simple list might be sufficient for the moment, but if this repository grows, you will need a way to search for particulat boxes. Is there anything planned yet to group/classify and annotate biobox functionalities in a standardized way?
@DSchober you are right, currently we are only maintaining a plain list. Bioboxes tries to follow the approach "by users for users" and thus we will have to come up with a more accessible and detailed index data structure which users can contribute to. Since our central hub currently is the GitHub project, I think that YAML/JSON files (over HTTPS with clients) will be a good start.
@fungs There is a YAML document created by @pbelmann here -https://github.com/bioboxes/data/blob/master/images.yml
@DSchober We have discussed using signatures as a way to classify bioboxes - bioboxes/rfc#9. This would be a way to classify each biobox based on the inputs it accepts and the outputs it returns.
Idea – we could add this gitter room to the bioboxes.org homepage using the new sidecar widget: https://sidecar.gitter.im/ & https://github.com/gitterHQ/sidecar
And I'll take a look at the widget, but I'm not too familiar with such stuff...
Creating the biobox?