inst/script/makeTxDbs.R

In jmacdon/GenomicFeatures: Conveniently import and query gene models

### 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")
}
}