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From: "Cook, Malcolm" <MEC@stowers.org>
To: "guix-devel@gnu.org" <guix-devel@gnu.org>
Subject: guix and mirroring dataset
Date: Mon, 17 May 2021 19:04:15 +0000	[thread overview]
Message-ID: <DM6PR20MB3410FBC7EB2A4F230F19365CBE2D9@DM6PR20MB3410.namprd20.prod.outlook.com> (raw)

HI,

Does the guix project and members suggest best guix-ish practices for managing on premise mirrors of large file-based data-sets such as appear in genomics HPC evironments?

Perhaps a guix-ish response to [Go Get Data \(GGD\) is a framework that facilitates reproducible access to genomic data](https://www.nature.com/articles/s41467-021-22381-z)

That would build on GWL?

Use cases would be, e.g. download/sync selected (versions of) genomes from Ensembl/NCBI etc and index them for Blast, blat, bowtie{2}, bwa, STAR, GMAP, HiSAT, IGV, BioConductor, etc...

I see much that addresses analysis workflows, such as
 -  [Reproducible genomics analysis pipelines with GNU Guix](https://www.biorxiv.org/content/10.1101/298653v2.full)
 - [Scalable Workflows and Reproducible Data Analysis for Genomics](https://pubmed.ncbi.nlm.nih.gov/31278683/)
 - [PiGx: reproducible genomics analysis pipelines with GNU Guix](https://academic.oup.com/gigascience/article/7/12/giy123/5114263)

Am I missing similar efforts toward maintaining an up-to-date catalog of the genomic resources that such workflows require?

Thanks!

Malcolm Cook
Database Applications Manager
Stowers Institute for Medical Research
Kansas City, MO  USA



             reply	other threads:[~2021-05-17 19:35 UTC|newest]

Thread overview: 4+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2021-05-17 19:04 Cook, Malcolm [this message]
  -- strict thread matches above, loose matches on Subject: below --
2021-05-27  0:24 guix and mirroring dataset zimoun
2021-05-27  4:37 ` Cook, Malcolm
2021-05-27 12:57   ` zimoun

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