leipzig

import tiledb
import tiledbvcf
import numpy as np


cloud_uri = "tiledb://TileDB-Inc/vcf-1kg-dragen-v376"

# This is the config I need to pass
cloud_config = tiledb.Config()
cloud_cfg = tiledbvcf.ReadConfig(tiledb_config=cloud_config)

leipzig

function mycd()
{
    #if this directory is writable then write to directory-based history file
    #otherwise write history in the usual home-based history file                    
    tmpDir=$PWD
    echo "#"`date '+%s'` >> $HISTFILE
    echo $USER' has exited '$PWD' for '$@ >> $HISTFILE
    builtin cd "$@" # do actual cd
    if [ -w $PWD ]; then export HISTFILE="$PWD/.dir_bash_history"; touch $HISTFILE; chmod --silent 777 $HISTFILE;
    else export HISTFILE="$HOME/.bash_history";

leipzig

- ABRA2:
  - https://igor.sbgenomics.com/raw/admin/sbg-public-data/abra2-12-germline/5
  - https://igor.sbgenomics.com/raw/admin/sbg-public-data/abra2-12-somatic/2
- Admixture:
  - https://igor.sbgenomics.com/raw/admin/sbg-public-data/admixture-1-3-0/4
- AmpliconQC:
  - https://igor.sbgenomics.com/raw/admin/sbg-public-data/sbg-ampliconqc-amplicon-coverage/1
  - https://igor.sbgenomics.com/raw/admin/sbg-public-data/sbg-ampliconqc-coverage-heatmap/1
  - https://igor.sbgenomics.com/raw/admin/sbg-public-data/sbg-ampliconqc-mark-failed-amplicons/1
  - https://igor.sbgenomics.com/raw/admin/sbg-public-data/sbg-ampliconqc-merge-coverage-beds/1

leipzig

#!/usr/bin/expect
set PASSWD "<<yourpass>>"
set timeout 3
spawn /opt/cisco/anyconnect/bin/vpn connect vpn.drexel.edu
expect "Group:"
send -- "0\r"
expect "*Username:*"
send -- "<<yourusername>>\r"
expect "*Password:*"
send -- "$PASSWD\r"

leipzig

#bin  chrom	chromStart	chromEnd	ix	n	size	type	bridge
0	chr1	124535434	142535434	1271	N	18000000	heterochromatin	no
23	chr1	121535434	124535434	1270	N	3000000	centromere	no
76	chr1	3845268	3995268	47	N	150000	contig	no
85	chr1	13219912	13319912	154	N	100000	contig	no
89	chr1	17125658	17175658	196	N	50000	clone	yes
101	chr1	29878082	30028082	337	N	150000	contig	no
188	chr1	120697156	120747156	1263	N	50000	clone	yes
188	chr1	120936695	121086695	1265	N	150000	contig	no
188	chr1	121485434	121535434	1269	N	50000	clone	no

leipzig

mz<-c('007','011','017','020','025','046','076','077','090','102','104')
sa<-c('008', '017', '037', '058', '069', '109', '097', '102','028')
jl<-c('075','060','061','106','066','070','104','059','017','001','015','014','038','010','005','039','006','020','031','094')

rn<-str_pad(seq(1,109), 3, pad = "0")
pics<-data.frame(id=rn,mz=FALSE,sa=FALSE,jl=FALSE)

pics[pics$id %in% mz,"mz"]<-TRUE
pics[pics$id %in% sa,"sa"]<-TRUE
pics[pics$id %in% jl,"jl"]<-TRUE

leipzig

#!/usr/bin/perl
use strict;
use Carp;
use Carp::Assert;
use Getopt::Std;
use File::Slurp;

my %opt;
my $opt_string = 'o:d:rh';

leipzig

python -c 'import rpy2.robjects as robjects'

this is almost certainly caused by conda-forge
to fix
conda install -c r r-base

leipzig

{
  "input_file": {
        "class": "File",
        "path": "https://raw.githubusercontent.com/briandoconnor/dockstore-tool-md5sum/master/md5sum.input"
    },
    "output_file": {
        "class": "File",
        "path": "s3://panoramabatch/md5sum.txt"
    }
}

leipzig

#requires 24.4 or higher, just use conda version 
M-x list-packages
C-v to scroll down
hit return on desired packages
C-x o to switch panes
go to [Install] hit return