Bioconductor / BSgenome

Software infrastructure for efficient representation of full genomes and their SNPs
https://bioconductor.org/packages/BSgenome
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Support for canFam4 #71

Open isilta opened 12 months ago

hpages commented 11 months ago

Thanks for the PR.

Note that starting with BioC 3.17, we're moving away from seed files and BSgenome::forgeBSgenomeDataPkg(). The new recommended way to forge a BSgenome data package is by using the BSgenomeForge package:

library(BSgenomeForge)

forgeBSgenomeDataPkgFromUCSC(genome="canFam4", organism="Canis lupus familiaris", pkg_maintainer="Jane Doe <janedoe@gmail.com>")
# trying URL 'http://hgdownload.cse.ucsc.edu/goldenPath/canFam4/bigZips/canFam4.2bit'
# Content type 'unknown' length 651703337 bytes (621.5 MB)
# ==================================================
# downloaded 621.5 MB
# 
# Creating package in ./BSgenome.Cfamiliaris.UCSC.canFam4 

See ?forgeBSgenomeDataPkgFromUCSC for more information.

Cheers, H.