Open donaldcampbelljr opened 7 months ago
Should we also add the common ones to our R dependency installation script?
# build BSgenome package ID to check whether it's installed
if ( startsWith(genome, "T2T")){
BSg = "BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0"
} else {
if (startsWith(genome, "hg") | startsWith(genome, "grch")) {
orgName = "Hsapiens"
} else if (startsWith(genome, "mm") | startsWith(genome, "grcm")){
orgName = "Mmusculus"
} else if (startsWith(genome, "dm")){
orgName = "Dmelanogaster"
} else if (startsWith(genome, "ce")){
orgName = "Celegans"
} else if (startsWith(genome, "danRer")){
orgName = "Drerio"
} else if (startsWith(genome, "TAIR")){
orgName = "Athaliana"
} else {
orgName = "Undefined"
}
BSg = paste0("BSgenome.", orgName , ".UCSC.", genome)
}
BSgm = paste0(BSg, ".masked")
In installRdeps.R
?
Currently, the pipeline may skip calculating GC content if it cannot find the associated BSGenoma package in the namespace. Unfortunately, it does not log this and silently skips attempting to calculate the GC content:
https://github.com/databio/bedboss/blob/b23c0a7dff112b99c7e5b0c3f08ebeb74a3fd74f/bedboss/bedstat/tools/regionstat.R#L95-L98
https://github.com/databio/bedboss/blob/b23c0a7dff112b99c7e5b0c3f08ebeb74a3fd74f/bedboss/bedstat/tools/regionstat.R#L188-L215
Simple solution would be to remove the
quietly=TRUE
from line 97, so that we capture this info: