Hi everyone! We are currently preparing the last steps for the first official release of nf-co.re/diseasemodulediscovery/dev For this, we migrated all containers to seqera or biocontainers, but for three of them, this is not possible, as the tools rely on unpackaged scripts, which need to be included into the containers. Because of this, we followed the instructions provided here: nf-co.re/docs/…/custom_containers The containers are now hosted on my personal docker hub and it would be amazing, if someone could transfer them to the official nf-core quay.io Thanks a lot in advance!

# DIAMOnD
docker pull kerstingjohannes/diamond:1.0.0-2437974
docker tag  kerstingjohannes/diamond:1.0.0-2437974 <http://quay.io/nf-core/diamond:1.0.0-2437974|quay.io/nf-core/diamond:1.0.0-2437974>
docker push <http://quay.io/nf-core/diamond:1.0.0-2437974|quay.io/nf-core/diamond:1.0.0-2437974>

# ROBUST
docker pull kerstingjohannes/robust:1.0.0-e8861de
docker tag  kerstingjohannes/robust:1.0.0-e8861de <http://quay.io/nf-core/robust:1.0.0-e8861de|quay.io/nf-core/robust:1.0.0-e8861de>
docker push <http://quay.io/nf-core/robust:1.0.0-e8861de|quay.io/nf-core/robust:1.0.0-e8861de>

# BioPAX Validator
docker pull kerstingjohannes/biopax-validator:6.0.0
docker tag  kerstingjohannes/biopax-validator:6.0.0 <http://quay.io/nf-core/biopax-validator:6.0.0|quay.io/nf-core/biopax-validator:6.0.0>
docker push <http://quay.io/nf-core/biopax-validator:6.0.0|quay.io/nf-core/biopax-validator:6.0.0>

Are these scripts actual packaged and published tools? If not are they simple single-file scripts?

DIAMOnD and ROBUST are single file scripts (ROBUST are actually a couple of scripts) of published tools (in journals). They have their own software dependencies but the authors never packaged them into python packages or something similar BioPAX validator is packaged software, but is packaged as a jar which we include into the container

Are the Dockerfiles published anywhere?

The dockerfiles are publicly available within the module directories in our pipeline: Diamond: github.com/nf-core/diseasemodulediscovery/blob/…/Dockerfile Robust: github.com/nf-core/diseasemodulediscovery/blob/…/Dockerfile Biopax validator: github.com/nf-core/diseasemodulediscovery/blob/…/Dockerfile But there are no "official" dockerfiles published by the tool developers

I think we would ask if there is a specific reason these cannot be put into

conda

, or potentially in the case of single-script tools, into the pipeline

bin

and used with a generic e.g.

python

container? nf-core hosting should really be a last-resort

I see. We already use conda for deploying tools wherever possible. But these three containers are already the ones where an installation through conda or pip is really not possible. We could also host the containers our self, but the documentation I linked states, that the nf-core qua.io is the prefered option to ensure long term availability. I personally do not think there are specific reasons why these tools cannot be on conda. Its probably just that the original developers never put them there. DIAMOnD could work as a single script in bin, but that would completely detach the code form the original repo. It has not seen a lot of activity in recent years, but using the container, it is at least transparent which specific commit the pipeline uses, should there be updates in the future.

I think it would be preferred to try and have these tools put into bioconda if possible. It should be fine to write bioconda recipes for these even if you are not the authors, and we have #CM46YC6BZ where you can ask if you have any issues or concerns about that. If after that there are still issues we would reassess if these custom containers are the best route.

Ok, we will give it a try. Thanks for your support!

pip works too