from fastq file to igv

~/Library/Preferences/com.apple.LaunchServices/com.apple.launchservices.secure.plist

$sleepDuration = Get-Random 2,3
$ps = [powershell]::Create().AddScript("Start-Sleep -Seconds $sleepDuration; 'Done!'")

# execute it asynchronously
$handle = $ps.BeginInvoke()

# Wait 2500 milliseconds for it to finish
if(-not $handle.AsyncWaitHandle.WaitOne(2500)){
    throw "timed out"
    return
}

# WaitOne() returned $true, let's fetch the result
$result = $ps.EndInvoke($handle)

return $result

#!/bin/bash    
wlan=`/sbin/ifconfig wlan0 | grep inet\ addr | wc -l`    
if [ $wlan -eq 0 ]; then    
    /sbin/ifdown wlan0 && /sbin/ifup wlan0
else    
    echo interface is up    
fi


# Then chmod 555 /root/checkwanup and add it to your crontab:

crontab -e
*/15 * * * * /bin/bash /root/checkwanup

shopt -s direxpand
complete -r cd

./aw-server > output.log 2>&1 &

cat >> ~/.inputrc <<'EOF'
"\e[A": history-search-backward
"\e[B": history-search-forward
EOF

# then
bind -f  ~/.inputrc

command1; command2

minimap2 -a /home/rezaeir/NanoporeData/ont-guppy/bin/17-05-2021-cas9-drunkCas9-combined/ref/HSV_US9_ref.fasta HSV-US9-Cas9-0.001.fastq.gz > HSV-US9-Cas9-0.001.sam

samtools view -S -b HSV-US9-Cas9-0.001.sam > HSV-US9-Cas9-0.001.bam

samtools view -b -F 4 HSV-US9-Cas9-0.001.bam > HSV-US9-Cas9-0.001.mapped.bam

samtools sort -@ 16 HSV-US9-Cas9-0.001.mapped.bam > HSV-US9-Cas9-0.001.mapped.sorted.bam

samtools index -@ 16 HSV-US9-Cas9-0.001.mapped.sorted.bam

sudo service systemd-logind restart

$ ls -l /proc/self/fd/ <<< "TEST"
total 0
lr-x------ 1 user1 user1 64 Aug 20 13:43 0 -> /tmp/sh-thd.761Lj9 (deleted)
lrwx------ 1 user1 user1 64 Aug 20 13:43 1 -> /dev/pts/4
lrwx------ 1 user1 user1 64 Aug 20 13:43 2 -> /dev/pts/4
lr-x------ 1 user1 user1 64 Aug 20 13:43 3 -> /proc/10068/fd

sudo /System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Resources/kickstart \
-activate -configure -access -on \
-clientopts -setvnclegacy -vnclegacy yes \
-clientopts -setvncpw -vncpw mypasswd \
-restart -agent -privs -all

sudo /System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Resources/kickstart \
-deactivate -configure -access -off

sudo /System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Resources/kickstart -deactivate -configure -access -off

sudo /System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Resources/kickstart \
 -activate -configure -access -on \
 -configure -allowAccessFor -allUsers \
 -configure -restart -agent -privs -all

prompt=$(sudo -nv 2>&1)
if [ $? -eq 0 ]; then
  # exit code of sudo-command is 0
  echo "has_sudo__pass_set"
elif echo $prompt | grep -q '^sudo:'; then
  echo "has_sudo__needs_pass"
else
  echo "no_sudo"
fi