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Mon, 17 May 2021 19:04:15 +0000 From: "Cook, Malcolm" To: "guix-devel@gnu.org" Subject: guix and mirroring dataset Thread-Topic: guix and mirroring dataset Thread-Index: AddLTI0U9/2lNIDpQS2KQgjH7Qi+iQ== Date: Mon, 17 May 2021 19:04:15 +0000 Message-ID: Accept-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: x-originating-ip: [65.26.91.244] x-ms-publictraffictype: Email x-ms-office365-filtering-correlation-id: fd08814f-a853-426f-d97a-08d9196690a5 x-ms-traffictypediagnostic: DM6PR20MB2442: x-microsoft-antispam-prvs: x-ms-oob-tlc-oobclassifiers: OLM:4941 x-ms-exchange-senderadcheck: 1 x-microsoft-antispam: BCL:0 x-microsoft-antispam-message-info: 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 x-forefront-antispam-report: CIP:255.255.255.255; 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Perhaps a guix-ish response to [Go Get Data \(GGD\) is a framework that fac= ilitates reproducible access to genomic data](https://www.nature.com/articl= es/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.bi= orxiv.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://a= cademic.oup.com/gigascience/article/7/12/giy123/5114263) Am I missing similar efforts toward maintaining an up-to-date catalog of th= e genomic resources that such workflows require? Thanks! Malcolm Cook Database Applications Manager Stowers Institute for Medical Research Kansas City, MO USA