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### This function is called from makeTerminalDBPkgs.R which is part of the
### release build code base. It creates new TxDb packages for a release and
### updates existing packages that have modified tracks.
### Check for new or updated tracks at
### https://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=587155737_kHXGzURQSTDan47Ux2E8zNtqcI0A
TxDbPackagesForRelease <-
function(version,
destDir='.',
maintainer= paste0("Bioconductor Package Maintainer ",
"<maintainer@bioconductor.org>"),
author="Bioconductor Core Team")
{
## New live tracks for Bioconductor 3.10
cat("building bosTau9 \n")
makeTxDbPackageFromUCSC(version=version,
maintainer=maintainer,
author=author,
destDir=destDir,
genome="bosTau9",
tablename="refGene")
cat("building galGal6 \n")
makeTxDbPackageFromUCSC(version=version,
maintainer=maintainer,
author=author,
destDir=destDir,
genome="galGal6",
tablename="refGene")
cat("building rheMac10 \n")
makeTxDbPackageFromUCSC(version=version,
maintainer=maintainer,
author=author,
destDir=destDir,
genome="rheMac10",
tablename="refGene")
cat("building panTro6 \n")
makeTxDbPackageFromUCSC(version=version,
maintainer=maintainer,
author=author,
destDir=destDir,
genome="panTro6",
tablename="refGene")
if(FALSE) {
## Update live tracks for Bioconductor 3.10
cat("building bosTau8 \n")
makeTxDbPackageFromUCSC(version=version,
maintainer=maintainer,
author=author,
destDir=destDir,
genome="bosTau8",
tablename="refGene")
cat("building canFam3 \n")
makeTxDbPackageFromUCSC(version=version,
maintainer=maintainer,
author=author,
destDir=destDir,
genome="canFam3",
tablename="refGene")
cat("building galGal4 \n")
makeTxDbPackageFromUCSC(version=version,
maintainer=maintainer,
author=author,
destDir=destDir,
genome="galGal4",
tablename="refGene")
cat("building galGal5 \n")
makeTxDbPackageFromUCSC(version=version,
maintainer=maintainer,
author=author,
destDir=destDir,
genome="galGal5",
tablename="refGene")
cat("building hg38 \n")
makeTxDbPackageFromUCSC(version=version,
maintainer=maintainer,
author=author,
destDir=destDir,
genome="hg38",
tablename="knownGene")
cat("building rheMac3 \n")
makeTxDbPackageFromUCSC(version=version,
maintainer=maintainer,
author=author,
destDir=destDir,
genome="rheMac3",
tablename="refGene")
cat("building rheMac8 \n")
makeTxDbPackageFromUCSC(version=version,
maintainer=maintainer,
author=author,
destDir=destDir,
genome="rheMac8",
tablename="refGene")
cat("building mm10 \n")
makeTxDbPackageFromUCSC(version=version,
maintainer=maintainer,
author=author,
destDir=destDir,
genome="mm10",
tablename="knownGene")
cat("building panTro4 \n")
makeTxDbPackageFromUCSC(version=version,
maintainer=maintainer,
author=author,
destDir=destDir,
genome="panTro4",
tablename="refGene")
cat("building panTro5 \n")
makeTxDbPackageFromUCSC(version=version,
maintainer=maintainer,
author=author,
destDir=destDir,
genome="panTro5",
tablename="refGene")
cat("building rn5 \n")
makeTxDbPackageFromUCSC(version=version,
maintainer=maintainer,
author=author,
destDir=destDir,
genome="rn5",
tablename="refGene")
cat("building susScr11 \n")
makeTxDbPackageFromUCSC(version=version,
maintainer=maintainer,
author=author,
destDir=destDir,
genome="susScr11",
tablename="refGene")
cat("building susScr3 \n")
makeTxDbPackageFromUCSC(version=version,
maintainer=maintainer,
author=author,
destDir=destDir,
genome="susScr3",
tablename="refGene")
}
}
|
