RefGenie - add assets currently used from AWS-iGenomes #1086

ewels · 2021-05-18T08:04:45Z

Split from #592, related directly to #1084

We want to transition away from using AWS-iGenomes to using the central RefGenie server(s) to host reference genome assets for the nf-core pipelines. To do this, we need to make sure that everything we currently have is available on a AWS refgenie server somewhere. Once all assets are mirrored we can do a clean swap in the config.

Going from igenomes.config, here is a check-list:

Summary of genomes

Detailed version with asset types

From @nsheff:

For updating: We drive the server instances off a git repository, here: https://github.com/refgenie/refgenomes.databio.org

RIght now, it's semi-automated. Eventually we want it to be that you just update the repo with a PR, and when merged it will deploy automatically. For now, though, we have to build the things manually, but it's all scripted from that repository. The asses are all just annotated with a PEP. So, to add a genome you'd add it to this CSV file: https://github.com/refgenie/refgenomes.databio.org/blob/master/asset_pep/genome_descriptions.csv

Then you'd add whatever inputs are required to build the assets to this file: https://github.com/refgenie/refgenomes.databio.org/blob/master/asset_pep/recipe_inputs.csv

See also:

The text was updated successfully, but these errors were encountered:

KevinMenden · 2021-05-28T11:21:38Z

stolarczyk · 2021-07-19T12:53:55Z

@KevinMenden, I can help put together the refgenie asset recipes for the missing asset types. Where can I find commands used to create these?

maxulysse · 2021-07-19T13:00:45Z

Needs more data than that for Sarek (cf: https://github.com/nf-core/sarek/blob/05194ed421d7fef6b7cef05fe267a95d8ceb4d6c/conf/igenomes.config#L36-L57)

ewels · 2022-06-17T17:57:01Z

TODO:

Still to add:

bed12 - add bed12 recipe refgenie/recipes#1

These can be added as attributes to eg. the Fast file rather than dedicated uploads:

mito_name
macs_gsize
Add attributes mito_name and macs_gsize to fasta asset refgenie/recipes#2

Readme can probably be skipped, as RefGenie hopefully already has enough provenance for assets.

ewels assigned KevinMenden May 18, 2021

ewels added the template nf-core pipeline/component template label May 18, 2021

This was referenced May 18, 2021

RefGenie integration #592

Closed

Use RefGenie for pipeline template genomes.conf config #1084

Open

RefGenie - add assets currently used from AWS-iGenomes #1085

Closed

KevinMenden mentioned this issue Jul 29, 2021

Refgenie Integration (Overview) #1239

Open

ewels mentioned this issue Mar 1, 2022

Feature request: new rat reference mRatBN7.2 ewels/AWS-iGenomes#15

Open

ewels assigned mirpedrol and ErikDanielsson and unassigned KevinMenden Jun 17, 2022

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RefGenie - add assets currently used from AWS-iGenomes #1086

RefGenie - add assets currently used from AWS-iGenomes #1086

ewels commented May 18, 2021 •

edited by mirpedrol

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KevinMenden commented May 28, 2021 •

edited

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stolarczyk commented Jul 19, 2021

maxulysse commented Jul 19, 2021

ewels commented Jun 17, 2022 •

edited by mirpedrol

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RefGenie - add assets currently used from AWS-iGenomes #1086

RefGenie - add assets currently used from AWS-iGenomes #1086

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ewels commented May 18, 2021 • edited by mirpedrol Loading

KevinMenden commented May 28, 2021 • edited Loading

stolarczyk commented Jul 19, 2021

maxulysse commented Jul 19, 2021

ewels commented Jun 17, 2022 • edited by mirpedrol Loading

ewels commented May 18, 2021 •

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KevinMenden commented May 28, 2021 •

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ewels commented Jun 17, 2022 •

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