wrapBaseDBPackages <- function (dbPath = "/mnt/cpb_anno/mcarlson/proj/mcarlson/sqliteGen/annosrc/db/",
destDir = ".",
version ){
#human.db0
vals <- list(ANNOBJPREFIX="human",
ORGANISM="Homo sapiens",
SPECIES="human",
AUTHOR="Marc Carlson, Nianhua Li, Herve Pages",
PKGVERSION=version,
LIC="The Artistic License, Version 2.0",
BIOCVIEWS="AnnotationData, Homo_sapiens",
ANNDBIVERSION="1.1.15",
MAINTAINER="Bioconductor Package Maintainer <maintainer@bioconductor.org>")
pkgName= paste(vals[["ANNOBJPREFIX"]],".db0",sep="")
template=paste(system.file(package = "AnnotationForge"), "/AnnDbPkg-templates/BASEPKG.DB", sep="")
chipSrcFile = paste(dbPath,"chipsrc_human.sqlite",sep="")
chipMapSrcFile = paste(dbPath,"chipmapsrc_human.sqlite",sep="")
makeBasePackage(chipSrcFile, chipMapSrcFile, pkgName, destDir, template, vals)
#mouse.db0
vals <- list(ANNOBJPREFIX="mouse",
ORGANISM="Mus musculus",
SPECIES="mouse",
AUTHOR="Marc Carlson, Nianhua Li, Herve Pages",
PKGVERSION=version,
LIC="The Artistic License, Version 2.0",
BIOCVIEWS="AnnotationData, Mus_musculus",
ANNDBIVERSION="1.1.15",
MAINTAINER="Bioconductor Package Maintainer <maintainer@bioconductor.org>")
pkgName= paste(vals[["ANNOBJPREFIX"]],".db0",sep="")
template=paste(system.file(package = "AnnotationForge"), "/AnnDbPkg-templates/BASEPKG.DB", sep="")
chipSrcFile = paste(dbPath,"chipsrc_mouse.sqlite",sep="")
chipMapSrcFile = paste(dbPath,"chipmapsrc_mouse.sqlite",sep="")
makeBasePackage(chipSrcFile, chipMapSrcFile, pkgName, destDir, template, vals)
#rat.db0
vals <- list(ANNOBJPREFIX="rat",
ORGANISM="Rattus norvegicus",
SPECIES="rat",
AUTHOR="Marc Carlson, Nianhua Li, Herve Pages",
PKGVERSION=version,
LIC="The Artistic License, Version 2.0",
BIOCVIEWS="AnnotationData, Rattus_norvegicus",
ANNDBIVERSION="1.1.15",
MAINTAINER="Bioconductor Package Maintainer <maintainer@bioconductor.org>")
pkgName= paste(vals[["ANNOBJPREFIX"]],".db0",sep="")
template=paste(system.file(package = "AnnotationForge"), "/AnnDbPkg-templates/BASEPKG.DB", sep="")
chipSrcFile = paste(dbPath,"chipsrc_rat.sqlite",sep="")
chipMapSrcFile = paste(dbPath,"chipmapsrc_rat.sqlite",sep="")
makeBasePackage(chipSrcFile, chipMapSrcFile, pkgName, destDir, template, vals)
#fly.db0
vals <- list(ANNOBJPREFIX="fly",
ORGANISM="Drosophila melanogaster",
SPECIES="fly",
AUTHOR="Marc Carlson, Nianhua Li, Herve Pages",
PKGVERSION=version,
LIC="The Artistic License, Version 2.0",
BIOCVIEWS="AnnotationData, Drosophila_melanogaster",
ANNDBIVERSION="1.1.15",
MAINTAINER="Bioconductor Package Maintainer <maintainer@bioconductor.org>")
pkgName= paste(vals[["ANNOBJPREFIX"]],".db0",sep="")
template=paste(system.file(package = "AnnotationForge"), "/AnnDbPkg-templates/BASEPKG.DB", sep="")
chipSrcFile = paste(dbPath,"chipsrc_fly.sqlite",sep="")
chipMapSrcFile = paste(dbPath,"chipmapsrc_fly.sqlite",sep="")
makeBasePackage(chipSrcFile, chipMapSrcFile, pkgName, destDir, template, vals)
#yeast.db0
vals <- list(ANNOBJPREFIX="yeast",
ORGANISM="Saccharomyces cerevisiae",
SPECIES="yeast",
AUTHOR="Marc Carlson, Nianhua Li, Herve Pages",
PKGVERSION=version,
LIC="The Artistic License, Version 2.0",
BIOCVIEWS="AnnotationData, Saccharomyces_cerevisiae",
ANNDBIVERSION="1.1.15",
MAINTAINER="Bioconductor Package Maintainer <maintainer@bioconductor.org>")
pkgName= paste(vals[["ANNOBJPREFIX"]],".db0",sep="")
template=paste(system.file(package = "AnnotationForge"), "/AnnDbPkg-templates/BASEPKG.DB", sep="")
chipSrcFile = paste(dbPath,"chipsrc_yeast.sqlite",sep="")
# chipMapSrcFile = paste(dbPath,"chipmapsrc_yeast.sqlite",sep="")
chipMapSrcFile = NULL
makeBasePackage(chipSrcFile, pkgName=pkgName, destDir=destDir, template=template, vals=vals)
#arabidopsis.db0
vals <- list(ANNOBJPREFIX="arabidopsis",
ORGANISM="Arabidopsis thaliana",
SPECIES="arabidopsis",
AUTHOR="Marc Carlson, Nianhua Li, Herve Pages",
PKGVERSION=version,
LIC="The Artistic License, Version 2.0",
BIOCVIEWS="AnnotationData, Arabidopsis_thaliana",
ANNDBIVERSION="1.1.15",
MAINTAINER="Bioconductor Package Maintainer <maintainer@bioconductor.org>")
pkgName= paste(vals[["ANNOBJPREFIX"]],".db0",sep="")
template=paste(system.file(package = "AnnotationForge"), "/AnnDbPkg-templates/BASEPKG.DB", sep="")
chipSrcFile = paste(dbPath,"chipsrc_arabidopsis.sqlite",sep="")
chipMapSrcFile = paste(dbPath,"chipmapsrc_arabidopsis.sqlite",sep="")
makeBasePackage(chipSrcFile, chipMapSrcFile, pkgName, destDir, template, vals)
#malaria.db0
vals <- list(ANNOBJPREFIX="malaria",
ORGANISM="Plasmodium falciparum",
SPECIES="malaria",
AUTHOR="Marc Carlson, Herve Pages",
PKGVERSION=version,
LIC="The Artistic License, Version 2.0",
BIOCVIEWS="AnnotationData, Plasmodium_falciparum",
ANNDBIVERSION="1.1.28",
MAINTAINER="Bioconductor Package Maintainer <maintainer@bioconductor.org>")
pkgName= paste(vals[["ANNOBJPREFIX"]],".db0",sep="")
template=paste(system.file(package = "AnnotationForge"), "/AnnDbPkg-templates/BASEPKG.DB", sep="")
chipSrcFile = paste(dbPath,"chipsrc_malaria.sqlite",sep="")
chipMapSrcFile = NULL
makeBasePackage(chipSrcFile, chipMapSrcFile, pkgName, destDir, template, vals)
#zebrafish.db0
vals <- list(ANNOBJPREFIX="zebrafish",
ORGANISM="Danio rerio",
SPECIES="zebrafish",
AUTHOR="Marc Carlson, Herve Pages",
PKGVERSION=version,
LIC="The Artistic License, Version 2.0",
BIOCVIEWS="AnnotationData, Danio_rerio",
ANNDBIVERSION="1.1.28",
MAINTAINER="Bioconductor Package Maintainer <maintainer@bioconductor.org>")
pkgName= paste(vals[["ANNOBJPREFIX"]],".db0",sep="")
template=paste(system.file(package = "AnnotationForge"), "/AnnDbPkg-templates/BASEPKG.DB", sep="")
chipSrcFile = paste(dbPath,"chipsrc_zebrafish.sqlite",sep="")
chipMapSrcFile = paste(dbPath,"chipmapsrc_zebrafish.sqlite",sep="")
makeBasePackage(chipSrcFile, chipMapSrcFile, pkgName, destDir, template, vals)
#canine.db0
vals <- list(ANNOBJPREFIX="canine",
ORGANISM="Canis familiaris",
SPECIES="canine",
AUTHOR="Marc Carlson, Herve Pages",
PKGVERSION=version,
LIC="The Artistic License, Version 2.0",
BIOCVIEWS="AnnotationData, Canis_familiaris",
ANNDBIVERSION="1.1.28",
MAINTAINER="Bioconductor Package Maintainer <maintainer@bioconductor.org>")
pkgName= paste(vals[["ANNOBJPREFIX"]],".db0",sep="")
template=paste(system.file(package = "AnnotationForge"), "/AnnDbPkg-templates/BASEPKG.DB", sep="")
chipSrcFile = paste(dbPath,"chipsrc_canine.sqlite",sep="")
chipMapSrcFile = paste(dbPath,"chipmapsrc_canine.sqlite",sep="")
makeBasePackage(chipSrcFile, chipMapSrcFile, pkgName, destDir, template, vals)
#bovine.db0
vals <- list(ANNOBJPREFIX="bovine",
ORGANISM="Bos taurus",
SPECIES="bovine",
AUTHOR="Marc Carlson, Herve Pages",
PKGVERSION=version,
LIC="The Artistic License, Version 2.0",
BIOCVIEWS="AnnotationData, Bos_taurus",
ANNDBIVERSION="1.1.28",
MAINTAINER="Bioconductor Package Maintainer <maintainer@bioconductor.org>")
pkgName= paste(vals[["ANNOBJPREFIX"]],".db0",sep="")
template=paste(system.file(package = "AnnotationForge"), "/AnnDbPkg-templates/BASEPKG.DB", sep="")
chipSrcFile = paste(dbPath,"chipsrc_bovine.sqlite",sep="")
chipMapSrcFile = paste(dbPath,"chipmapsrc_bovine.sqlite",sep="")
makeBasePackage(chipSrcFile, chipMapSrcFile, pkgName, destDir, template, vals)
#ecoliK12.db0
vals <- list(ANNOBJPREFIX="ecoliK12",
ORGANISM="Escherichia coli",
SPECIES="E coli K12 Strain",
AUTHOR="Marc Carlson, Herve Pages",
PKGVERSION=version,
LIC="The Artistic License, Version 2.0",
BIOCVIEWS="AnnotationData, Escherichia_coli",
ANNDBIVERSION="1.1.28",
MAINTAINER="Bioconductor Package Maintainer <maintainer@bioconductor.org>")
pkgName= paste(vals[["ANNOBJPREFIX"]],".db0",sep="")
template=paste(system.file(package = "AnnotationForge"), "/AnnDbPkg-templates/BASEPKG.DB", sep="")
chipSrcFile = paste(dbPath,"chipsrc_ecoliK12.sqlite",sep="")
chipMapSrcFile = paste(dbPath,"chipmapsrc_ecoliK12.sqlite",sep="")
makeBasePackage(chipSrcFile, chipMapSrcFile, pkgName, destDir, template, vals)
#ecoliSakai.db0
vals <- list(ANNOBJPREFIX="ecoliSakai",
ORGANISM="Escherichia coli",
SPECIES="E coli Sakai Strain",
AUTHOR="Marc Carlson, Herve Pages",
PKGVERSION=version,
LIC="The Artistic License, Version 2.0",
BIOCVIEWS="AnnotationData, Escherichia_coli",
ANNDBIVERSION="1.1.28",
MAINTAINER="Bioconductor Package Maintainer <maintainer@bioconductor.org>")
pkgName= paste(vals[["ANNOBJPREFIX"]],".db0",sep="")
template=paste(system.file(package = "AnnotationForge"), "/AnnDbPkg-templates/BASEPKG.DB", sep="")
chipSrcFile = paste(dbPath,"chipsrc_ecoliSakai.sqlite",sep="")
chipMapSrcFile = paste(dbPath,"chipmapsrc_ecoliSakai.sqlite",sep="")
makeBasePackage(chipSrcFile, chipMapSrcFile, pkgName, destDir, template, vals)
#worm.db0
vals <- list(ANNOBJPREFIX="worm",
ORGANISM="Caenorhabditis elegans",
SPECIES="worm",
AUTHOR="Marc Carlson, Herve Pages",
PKGVERSION=version,
LIC="The Artistic License, Version 2.0",
BIOCVIEWS="AnnotationData, Caenorhabditis_elegans",
ANNDBIVERSION="1.1.28",
MAINTAINER="Bioconductor Package Maintainer <maintainer@bioconductor.org>")
pkgName= paste(vals[["ANNOBJPREFIX"]],".db0",sep="")
template=paste(system.file(package = "AnnotationForge"), "/AnnDbPkg-templates/BASEPKG.DB", sep="")
chipSrcFile = paste(dbPath,"chipsrc_worm.sqlite",sep="")
chipMapSrcFile = paste(dbPath,"chipmapsrc_worm.sqlite",sep="")
makeBasePackage(chipSrcFile, chipMapSrcFile, pkgName, destDir, template, vals)
#pig.db0
vals <- list(ANNOBJPREFIX="pig",
ORGANISM="Sus scrofa",
SPECIES="pig",
AUTHOR="Marc Carlson, Herve Pages",
PKGVERSION=version,
LIC="The Artistic License, Version 2.0",
BIOCVIEWS="AnnotationData, Sus_scrofa",
ANNDBIVERSION="1.1.28",
MAINTAINER="Bioconductor Package Maintainer <maintainer@bioconductor.org>")
pkgName= paste(vals[["ANNOBJPREFIX"]],".db0",sep="")
template=paste(system.file(package = "AnnotationForge"), "/AnnDbPkg-templates/BASEPKG.DB", sep="")
chipSrcFile = paste(dbPath,"chipsrc_pig.sqlite",sep="")
chipMapSrcFile = paste(dbPath,"chipmapsrc_pig.sqlite",sep="")
makeBasePackage(chipSrcFile, chipMapSrcFile, pkgName, destDir, template, vals)
#chicken.db0
vals <- list(ANNOBJPREFIX="chicken",
ORGANISM="Gallus gallus",
SPECIES="chicken",
AUTHOR="Marc Carlson, Herve Pages",
PKGVERSION=version,
LIC="The Artistic License, Version 2.0",
BIOCVIEWS="AnnotationData, Gallus_gallus",
ANNDBIVERSION="1.1.28",
MAINTAINER="Bioconductor Package Maintainer <maintainer@bioconductor.org>")
pkgName= paste(vals[["ANNOBJPREFIX"]],".db0",sep="")
template=paste(system.file(package = "AnnotationForge"), "/AnnDbPkg-templates/BASEPKG.DB", sep="")
chipSrcFile = paste(dbPath,"chipsrc_chicken.sqlite",sep="")
chipMapSrcFile = paste(dbPath,"chipmapsrc_chicken.sqlite",sep="")
makeBasePackage(chipSrcFile, chipMapSrcFile, pkgName, destDir, template, vals)
## #yeastNCBI.db0
## vals <- list(ANNOBJPREFIX="yeastNCBI",
## ORGANISM="Saccharomyces cerevisiae",
## SPECIES="yeast",
## AUTHOR="Marc Carlson, Nianhua Li, Herve Pages",
## PKGVERSION=version,
## LIC="The Artistic License, Version 2.0",
## BIOCVIEWS="AnnotationData, Saccharomyces_cerevisiae",
## ANNDBIVERSION="1.1.28",
## MAINTAINER="Bioconductor Package Maintainer <maintainer@bioconductor.org>")
## pkgName= paste(vals[["ANNOBJPREFIX"]],".db0",sep="")
## template=paste(system.file(package = "AnnotationForge"), "/AnnDbPkg-templates/BASEPKG.DB", sep="")
## chipSrcFile = paste(dbPath,"chipsrc_yeastNCBI.sqlite",sep="")
## chipMapSrcFile = paste(dbPath,"chipmapsrc_yeastNCBI.sqlite",sep="")
## makeBasePackage(chipSrcFile, pkgName=pkgName, destDir=destDir, template=template, vals=vals)
#chimp.db0
vals <- list(ANNOBJPREFIX="chimp",
ORGANISM="Pan troglodytes",
SPECIES="chimp",
AUTHOR="Marc Carlson, Herve Pages",
PKGVERSION=version,
LIC="The Artistic License, Version 2.0",
BIOCVIEWS="AnnotationData, Pan_troglodytes",
ANNDBIVERSION="1.7.0",
MAINTAINER="Bioconductor Package Maintainer <maintainer@bioconductor.org>")
pkgName= paste(vals[["ANNOBJPREFIX"]],".db0",sep="")
template=paste(system.file(package = "AnnotationForge"), "/AnnDbPkg-templates/BASEPKG.DB", sep="")
chipSrcFile = paste(dbPath,"chipsrc_chimp.sqlite",sep="")
chipMapSrcFile = paste(dbPath,"chipmapsrc_chimp.sqlite",sep="")
makeBasePackage(chipSrcFile, chipMapSrcFile, pkgName, destDir, template, vals)
#rhesus.db0
vals <- list(ANNOBJPREFIX="rhesus",
ORGANISM="Macaca Mulatta",
SPECIES="rhesus",
AUTHOR="Marc Carlson, Herve Pages",
PKGVERSION=version,
LIC="The Artistic License, Version 2.0",
BIOCVIEWS="AnnotationData, Macaca_Mulatta",
ANNDBIVERSION="1.7.0",
MAINTAINER="Bioconductor Package Maintainer <maintainer@bioconductor.org>")
pkgName= paste(vals[["ANNOBJPREFIX"]],".db0",sep="")
template=paste(system.file(package = "AnnotationForge"), "/AnnDbPkg-templates/BASEPKG.DB", sep="")
chipSrcFile = paste(dbPath,"chipsrc_rhesus.sqlite",sep="")
chipMapSrcFile = paste(dbPath,"chipmapsrc_rhesus.sqlite",sep="")
makeBasePackage(chipSrcFile, chipMapSrcFile, pkgName, destDir, template, vals)
#anopheles.db0
vals <- list(ANNOBJPREFIX="anopheles",
ORGANISM="Anopheles gambiae",
SPECIES="anopheles",
AUTHOR="Marc Carlson, Herve Pages",
PKGVERSION=version,
LIC="The Artistic License, Version 2.0",
BIOCVIEWS="AnnotationData, Anopheles_gambiae",
ANNDBIVERSION="1.7.0",
MAINTAINER="Bioconductor Package Maintainer <maintainer@bioconductor.org>")
pkgName= paste(vals[["ANNOBJPREFIX"]],".db0",sep="")
template=paste(system.file(package = "AnnotationForge"), "/AnnDbPkg-templates/BASEPKG.DB", sep="")
chipSrcFile = paste(dbPath,"chipsrc_anopheles.sqlite",sep="")
chipMapSrcFile = paste(dbPath,"chipmapsrc_anopheles.sqlite",sep="")
makeBasePackage(chipSrcFile, chipMapSrcFile, pkgName, destDir, template, vals)
#xenopus.db0
vals <- list(ANNOBJPREFIX="xenopus",
ORGANISM="Xenopus laevis",
SPECIES="xenopus",
AUTHOR="Marc Carlson, Herve Pages",
PKGVERSION=version,
LIC="The Artistic License, Version 2.0",
BIOCVIEWS="AnnotationData, Xenopus_laevis",
ANNDBIVERSION="1.7.0",
MAINTAINER="Bioconductor Package Maintainer <maintainer@bioconductor.org>")
pkgName= paste(vals[["ANNOBJPREFIX"]],".db0",sep="")
template=paste(system.file(package = "AnnotationForge"), "/AnnDbPkg-templates/BASEPKG.DB", sep="")
chipSrcFile = paste(dbPath,"chipsrc_xenopus.sqlite",sep="")
chipMapSrcFile = paste(dbPath,"chipmapsrc_xenopus.sqlite",sep="")
makeBasePackage(chipSrcFile, chipMapSrcFile, pkgName, destDir, template, vals)
}
#makeBase Package is just a utility function to minimize code bloat.
makeBasePackage <- function(chipSrcFile = NULL,#No chipSrcFile = no package
chipMapSrcFile = NULL,#No chipMapSrcFile is sometimes ok
pkgName,
destDir,
template,
vals){
if(length(chipSrcFile)>0){
createPackage(pkgname=pkgName,
destinationDir=destDir,
originDir=template,
symbolValues=vals)
db_destDir = file.path(destDir,pkgName,"inst/extdata/")
if (!file.copy(chipSrcFile, db_destDir)){
stop("cannot copy file '", chipSrcFile, "' to '", db_destDir, "'")
}
if(length(chipMapSrcFile) > 0){
if (!file.copy(chipMapSrcFile, db_destDir)){
stop("cannot copy file '", chipMapSrcFile, "' to '", db_destDir, "'")
}
}
}
else{
stop("Cannot find the chipSrcFile to make the package.")
}
}
