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Add r-saige and regenie from bioconda
Hi all,
I would like to add bioconda containers for r-saige and regenie. I am not so sure how the relation between biocontainers and bioconda works. Do I have to make Dockerfiles and pull requests to this repository? or are you able to use the containers from quay?
https://quay.io/repository/biocontainers/r-saige?tab=tags https://quay.io/repository/biocontainers/regenie?tab=tags
Biocontainers link shows empty result so far:
- https://biocontainers.pro/#/tools/r-saige
- https://biocontainers.pro/#/tools/regenie
Hi, If there is a bioconda package, containers are automatically created and pushed to quay.io and integrated to "biocontainers"
Hi @osallou
what does that mean in practice on biocontainers side? Should I be able to query names of those packages in registry? (https://biocontainers.pro/#/registry) I have added both of those packages to bioconda just a few weeks ago, and if you check those biocontainers URLs they don't seem to include anything and it doesn't appear in registry search either. Am I misunderstanding something here?
nope, should appear in registry after merge in bioconda
@ypriverol do registry updates are ok?
@ypriverol @osallou maybe you could have some pointers where I could look to help solving this?
Hum thanks, but it is on your backend that fetch info from docker/conda repos. Yasset manages it don t think you can easilly fix the issue and pricess to fetch data is quite long.
@ypriverol some news on issue?
..i was just about to open a similar issue.. I added the first version of GUNC 2 months ago but it still doesn't appear in the biocontainers registry.. it seems that nothing new is being added right now? it also looks like no new updates for tools that are already in there are appearing..
the containers are built though, i can see them on quay.io for example, so it might be just whatever pulls the info into the website that has stopped working?
Something is wrong with the biocontainers organization in Quay.
Trying to fetch the biocontainers organization returns 504
https://quay.io/organization/biocontainers
Using API:
$ curl "https://quay.io/api/v1/repository?last_modified=true&namespace=biocontainers&popularity=true&public=true"
<html>
<head><title>504 Gateway Time-out</title></head>
<body bgcolor="white">
<center><h1>504 Gateway Time-out</h1></center>
<hr><center>nginx/1.12.1</center>
</body>
</html>
fetching from other Quay organizations works well
https://quay.io/organization/bitnami
Using API:
curl https://quay.io/api/v1/repository?last_modified=true&namespace=bitnami&popularity=true&public=true
May be biocontainers has too many entries to fetch
you are probably right there, if you leave out the last_modified parameter it returns before the query times out:
curl "https://quay.io/api/v1/repository?namespace=biocontainers&popularity=true&public=true"
{"repositories": [{"kind": "image", "name": "coreutils", "namespace": "biocontainers", "state": null, "is_public": true, "description": "# Coreutils\n\n> The gnu core utilities are the .........
Thanks @fullama. Removed that last_modified parameter from the pipeline. Hopefully the issue should be fixed after the pipeline finishes in couple of hours
Also, I wrote an email to Quay support. Hopefully they will address the issue.
You certainly have in api to manage pagination to avoid timeouts due to large number of containers. Maybe you hit timeout now or tgey reduced timeout on their side
Le jeu. 17 déc. 2020 à 15:27, Chakra [email protected] a écrit :
Thanks @fullama https://github.com/fullama. Removed that last_modified parameter from the pipeline. Hopefully the issue should be fixed after the pipeline finishes in couple of hours
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Well at least it seems to work for now.. its not a long term solution by any means but the packages that have been mentioned here have appeared.. so success! :) - thanks for sorting it out.. its very appreciated
the quay.io api doesnt seem to offer pagination in their API: https://docs.quay.io/api/swagger/#!/repository/listRepos ..at least not that i can see.. :-/
@fullama seems there is a next_page (or kind) parameter , don't know for limit per page