startup.R

.libPaths(unique(c("/gpfs/commons/groups/imielinski_lab/lib/R-4.0.2_KH", .libPaths())))

Sys.setenv(DEFAULT_BSGENOME = "/gpfs/commons/groups/imielinski_lab/DB/GATK/human_g1k_v37_decoy.chrom.sizes")
Sys.setenv(DEFAULT_GENOME = "/gpfs/commons/groups/imielinski_lab/DB/GATK/human_g1k_v37_decoy.chrom.sizes")

Sys.setenv(PATH = paste("~/software/bcftools-1.9", Sys.getenv("PATH"), sep = ":"))
Sys.setenv(BCFTOOLS_PLUGINS = "/gpfs/commons/groups/imielinski_lab/Software/bcftools-1.9/plugins")

startup();
library(withr)
library(skitools)
library(gGnome)
library(Flow)
library(dplyr)
library(bamUtils)
library(skidb)
library(naturalsort)
library(magrittr)
library(signature.tools.lib)
library(tidyr)
library(MASS)
library(khtools)
library(wesanderson)
forceload(.force = T)

## require3(
##     withr,
##     skitools,
##     gGnome,
##     Flow,
##     dplyr,
##     bamUtils,
##     skidb,
##     naturalsort,
##     magrittr,
##     signature.tools.lib,
##     tidyr,
##     MASS,
##     khtools,
##     wesanderson
## )

## source("~/lab/home/khadi/git/khscripts/patch_gtrack.R")

exprs = expression({
    brewer.master <- skitools::brewer.master
    `%$%` <- gUtils::`%$%`
    `%&%` <- gUtils::`%&%`
    ## `%Q%` <- gUtils::`%Q%`
    `%Q%` <- khtools::`%Q%`
    `%+%` <- gUtils::`%+%`
    `%-%` <- gUtils::`%-%`
    `%^%` <- gUtils::`%^%`
    width <- GenomicRanges::width
    reduce <- GenomicRanges::reduce
    between <- data.table::between
    setnames <- data.table::setnames
    select <- dplyr::select
    update <- Flow::update
    cache <- Flow::cache
    set <- data.table::set
    set_names <- rlang::set_names
    matches <- dplyr::matches
    n <- dplyr::n
    last <- dplyr::last
    first <- dplyr::first
    tailf <- khtools::tailf
    coalesce <- khtools::coalesce
    ppdf <- khtools::ppdf
    ppng <- khtools::ppng
    with_libpaths <- withr::with_libpaths
    with_options <- withr::with_options
    melt <- data.table::melt
    overwritefun(khtools::gr.flipstrand, gUtils::gr.flipstrand); gr.flipstrand <- khtools::gr.flipstrand
    .S3method("merge", "Junction", merge.Junction)
    registerS3method("merge", "Junction", merge.Junction, envir = globalenv())
    .S3method("dcast", "data.table", dcast.data.table)
    registerS3method("dcast", "data.table", dcast.data.table, envir = globalenv())
})

eix = seq(2, length(exprs[[1]]))
for (i in eix) {
    print(exprs[[1]][[i]])
    tryCatch({
        eval(exprs[[1]][[i]], envir = globalenv())
    }, error = function(e) NULL)
}

## tryCatch({
##     .S3method("merge", "Junction", merge.Junction)
##     registerS3method("merge", "Junction", merge.Junction, envir = parent.frame())
## }, error = function(e) NULL)



## tryCatch({
##     .S3method("dcast", "data.table", dcast.data.table)
##     registerS3method("dcast", "data.table", dcast.data.table, envir = parent.frame())
## }, error = function(e) NULL)