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Add r-saige and regenie from bioconda #392

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matuskosut opened this issue Nov 23, 2020 · 17 comments
Open

Add r-saige and regenie from bioconda #392

matuskosut opened this issue Nov 23, 2020 · 17 comments
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@ypriverol
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@matuskosut
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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:
@osallou
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osallou commented Nov 23, 2020

Hi,
If there is a bioconda package, containers are automatically created and pushed to quay.io and integrated to "biocontainers"

@matuskosut
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matuskosut commented Nov 23, 2020 •
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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?

@osallou
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osallou commented Nov 23, 2020

nope, should appear in registry after merge in bioconda

@ypriverol do registry updates are ok?

@ypriverol
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I will have a look today !!!

@matuskosut
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@ypriverol thanks for joining, hope you will manage to solve it

@matuskosut
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@ypriverol @osallou maybe you could have some pointers where I could look to help solving this?

@osallou
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osallou commented Dec 8, 2020

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?

@fullama
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fullama commented Dec 17, 2020

..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?

@osallou
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osallou commented Dec 17, 2020

sorry for this, I am trying to contact person in charge of registry

@ypriverol
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We are trying to fix the bug. Will be back to you soon.

@ypriverol ypriverol self-assigned this Dec 17, 2020
@ypriverol ypriverol added the bug label Dec 17, 2020
@chakrabandla
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chakrabandla commented Dec 17, 2020 •
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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

@fullama
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fullama commented Dec 17, 2020

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 .........

@chakrabandla
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chakrabandla commented Dec 17, 2020 •
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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.

@osallou
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osallou commented Dec 17, 2020 via email

@fullama
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fullama commented Dec 17, 2020

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.. :-/

@ypriverol
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We will contact quay.io team to find a better solution

@osallou
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osallou commented Dec 17, 2020

@fullama seems there is a next_page (or kind) parameter , don't know for limit per page

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@ypriverol @osallou @fullama @matuskosut @chakrabandla