track_job_ids = function(jids){
PS_OPTIONS$PS_JOB_IDS = c(getOption("PS_JOB_IDS", character()), jids)
}
#' Title
#'
#' @return
#'
#' @examples
#' treat_bam = "/slipstream/galaxy/uploads/working/qc_framework/output/MCF10A_H3K4AC_R1/MCF10A_H3K4AC_R1.bam"
#' ctrl_bam = "/slipstream/galaxy/uploads/working/qc_framework/output/MCF10A_input_R1/MCF10A_input_R1.bam"
#' psc = peaksat_config()
#' cmd = make_submit_cmd(psc, treat_bam, ctrl_bam)
#' sub_out = system(cmd, intern = TRUE)
#' sub_out
make_submit_cmd = function(psc,
treatment,
control,
submit_script = get_submit_script(),
hold_jid = NULL){
stat_arg = make_stat_arg(psc, out_dir = psc@out_dir)
if(is.null(hold_jid)){
hold_arg = character()
}else{
hold_arg = paste0(" -h ", hold_jid)
}
paste0("bash ",
submit_script,
" -m ",
psc@macs2_path,
" -st ",
psc@samtools_path,
" -t ",
treatment,
ifelse(is.null(control),
"",
paste0(" -c ",
control)),
ifelse(psc@is_PE,
" -pe ",
""
),
" -n ",
paste(sep = "_", sub(".bam", "", basename(treatment)), names(stat_arg)),
" ",
stat_arg,
" -js ",
psc@job_scheduler,
hold_arg)
}
#' Title
#'
#' @param psc A valid peaksat_config object
#' @param treat_bams Vector of ChIPseq bam files
#' @param ctrl_bams Vector of input bam files parallel to ChIPseq. If NULL, macs2 will be called without using an input file.
#' @param macs2_path
#' @param submit_script
#' @param await_completion
#'
#' @return
#' @export
#'
#' @examples
submit_peaksat_jobs = function(psc,
treat_bams,
ctrl_bams,
hold_jid_map = NULL,
await_completion = TRUE){
if(!is.null(ctrl_bams)){
if(length(ctrl_bams) != length(treat_bams)){
if(length(ctrl_bams) != 1){
stop("ctrl_bams must be same length as treat_bams or 1.")
}else{
ctrl_bams = rep(ctrl_bams, length(treat_bams))
}
}
}
if(any(!file.exists(treat_bams))){
if(is.null(hold_jid_map)){
stop("not all treat_bams exist!: ", paste(treat_bams[!file.exists(treat_bams)], collapse = ", "))
}else{
message("not all treat_bams exists, hopefully they will by time held jobs (hold_jid_map) finishes.")
message(paste(treat_bams[!file.exists(treat_bams)], collapse = ", "))
}
}
treat_bams = suppressWarnings(normalizePath(treat_bams))
if(!is.null(ctrl_bams)){
if(any(!file.exists(ctrl_bams))){
if(is.null(hold_jid_map)){
stop("not all ctrl_bams exist!: ", paste(ctrl_bams[!file.exists(ctrl_bams)], collapse = ", "))
}else{
message("not all ctrl_bams exists, hopefully they will by time held jobs (hold_jid_map) finishes.")
message(paste(ctrl_bams[!file.exists(ctrl_bams)], collapse = ", "))
}
}
ctrl_bams = suppressWarnings(normalizePath(ctrl_bams))
}
if(!is.null(hold_jid_map)){
names(hold_jid_map) = suppressWarnings(normalizePath(names(hold_jid_map)))
}
cmds = sapply(seq_along(treat_bams), function(i){
t_bam = treat_bams[i]
c_bam = ctrl_bams[i]
if(is.null(hold_jid_map)){
hold_jid = NULL
}else{
hold_jid = hold_jid_map[t_bam]
}
make_submit_cmd(psc = psc, treatment = t_bam, control = c_bam, hold_jid = hold_jid)
})
cmd_outs = sapply(cmds, function(cmd_sub){
qsub_str = system(cmd_sub, intern = TRUE)
qsub_str
})
jids = sapply(cmd_outs, function(cmd_out){
jid = capture_jid(cmd_out)
jid
})
PS_OPTIONS$PS_JOB_IDS = c(getOption("PS_JOB_IDS", character()), jids)
if(await_completion){
message(length(jids), " subset-callpeak jobs have been submitted to scheduler.\nWill await their completion before continuing.\nThis behavior can be controlled with 'await_completion = TRUE/FALSE'.\n'load_counts()' will not work properly until all jobs have finished.")
watch_jids(jids, psc@job_scheduler)
}else{
message(length(jids), " subset-callpeak jobs have been submitted to scheduler.\nUse watch_jids(PS_OPTIONS$PS_JOB_IDS) to monitor.\n'load_counts()' will not work properly until all jobs have finished.")
}
invisible(jids)
}
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