MVesuviusC

from: https://researchcomputing.princeton.edu/support/knowledge-base/rrstudio

9. How can I solve the following error?

Installing package into ‘/home/ceisgrub/R/x86_64-redhat-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") :
  [tcl] grab failed: window not viewable.
R is trying to display a list of mirrors via X11 forwarding so try unsetting DISPLAY before starting R:

MVesuviusC

function sacctRun() {
    sacct --format="user,jobid,jobname,node,state,ExitCode,start,end,maxrss" \
        | grep -v "COMPLETE\|FAIL\|CANCEL\|OUT_OF_ME" \
        | awk '$2 != "batch" && $2 != "extern" {print}'
}

get_maint_time () {
    maint_start=$(scontrol show -u root reservation \
                | perl -pe 's/\n/#/g' \
                | perl -pe 's/#ReservationName=/\n/g' \

MVesuviusC

 # open powershell
 Get-FileHash file_here.txt -Algorithm MD5

MVesuviusC

# record command line inputs/outputs
script logfile.txt

# type stuff 

exit

## Log is saved in logfile.txt

MVesuviusC

#capture groups
sed \
  -E 's/.+(GA.+CA).+/stuff_\1_stuff/' \
  /reference/homo_sapiens/hg19/ucsc_assembly/illumina_download/Sequence/WholeGenomeFasta/genome.fa \
  | head
  
  
  

MVesuviusC

ml picard/2.21.6-Java-11.0.2

java -jar \
    $EBROOTPICARD/picard.jar \
    ValidateSamFile \
    I=/gpfs0/scratch/mvc002/testTwoTumors/split_sams_2//S0149_1.sam \
    MODE=VERBOSE
    
    # Can optionally include ignore arguments to ignore specific error types
    IGNORE=MISSING_TAG_NM \

MVesuviusC

test <- parallel::mclapply(as.list(0:5), function(x) {
    print(x)
    if (x == 0) {
        stop("something didn't work for ", x)
    }
    return(1)
})

if (any(lapply(test, function(x) class(x) == "try-error") |> unlist())) {

MVesuviusC

If you get the error about [error] Barcode out of bounds during cellranger mkfastq:

Have to run bcl2fastq directly like I did in R0063

https://kb.10xgenomics.com/hc/en-us/articles/360038857411--error-Barcode-out-of-bounds-I1-0-14-or-I2-0-16-

MVesuviusC

Create new account environment variable on your windows machine named DISPLAY with value of localhost:0.0

Make sure mobaxterm is running (or whatever X11 you want)

In your "Configure SSH Hosts" menu, put this under each Host:
  ForwardX11 yes
  ForwardX11Trusted yes

MVesuviusC

# compare the contents of the commands slot between test and combined_data
cmp_seurat_cmds <- function(sobj_a,
                            sobj_b,
                            sobj_a_name = "sobj_a",
                            sobj_b_name = "sobj_b",
                            verbose = FALSE) {
    # Making a list here as not all of the contents of the arguments fit into a tibble
    # A list can accept any data type 
    diff_list <- list()
    for (step_ran in names(sobj_a@commands)) {