Remote desktop

Remote desktop can be used to not only work on the remote computer, but also copy clipboard and normal files between the remote computer and your local computer

Change settings in the connection

Remote Desktop Menu

Select “More” in Local Resources

Enable Local Discs

Locate your local drives

File Explorer Sidebar

File Explorer Sidebar - detail

WSL2 current setup: Name, volumes, environments

The WSL2 for bioinformatics is available as “Ubuntu” from the Start menu
The NAS is mounted automatically when you log in to keep the C:\ drive occupation minimal

Environments

• ‘bioinfo’ activated by ‘conda activate bioinfo’ contains the tools from the biostar handbook 2nd Edition for ChIPseq
• ‘py2’ activated by ‘conda activate py2’ contains the python version 2.7 to run the MACS tool

WSL2 basic interaction: get info from powershell

Check for instances human readible

wsl --list --verbose
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Get the GUID identification numbers:

Get-ChildItem "HKCU:\Software\Microsoft\Windows\CurrentVersion\Lxss" | ForEach-Object {
    $name = (Get-ItemProperty $_.PSPath).DistributionName
    [PSCustomObject]@{
        Name = $name
        Path = $_.Name
    }
}
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Use the {…} part = GUID to Find the BasePath to the distro:

Get-ItemProperty "HKCU:\Software\Microsoft\Windows\CurrentVersion\Lxss\<GUID>"
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WSL2 basic interaction: start stop WSL2 from powershell

Start:

wsl -d Ubuntu
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Stop Specfic distro:

wsl --terminate Ubuntu
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Stop all WSL linked processes:

wsl --shutdown
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WSL2 managment: WSL2 eating up too much space

The Ubuntu instance filled 175GB of space when trying to convert 16GB sra files to fastq using fasterq-dump
The issue seems to stem from a virtual disk of Ubuntu WSL2 instance not shrinking automatically

Shrink the volume manually

1. Enable the Hyper-V stuff using <Win>+<R>
2. type ‘optionalfeatures’
3. Find Hyper V and tick it active
4. Shutdown wsl --shutdown
5. Find a path to your ext4 virtual disk (Leica one is at: “C:\WSL\Ubutnu_01\ext4.vhdx”)
6. Compress in powershell run as administrator

Optimize-VHD -Path "C:\WSL\Ubuntu_01\ext4.vhdx" -Mode Full
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Note: Shrunk from 175GB to 50GB when tried first

WSL2 managment: Put a new instance on an SSD

1. in powershell: wsl --export Ubuntu E:\ubuntu_backup03.tar Note: Ubuntu is my distribution name, yours can be different
2. In case you want to transfer the instance unregister the old vesrsion wsl --unregister Ubuntu, in case you want to make new one no need to do it
3. wsl --import Ubuntu_biouser_new G:\WSL\ E:\ubuntu_backup03.tar --version 2
4. For the speed, nee do to this on an SSD, placed new 256GB SSD in the lowest SATA slot in Leica Comp

WSL2 managment: Restrict memory CPU and SWAP (not tested yet)

C:\Users\<YourUsername>\.wslconfig
[wsl2]
memory=4GB
processors=4
swap=0
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WSL2 managment: Automatic mounting of NAS

1. Install cifs-utils

sudo apt update
sudo apt install cifs-utils
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2. Check presence of the network drive

When you map network drive in windows the server name and folder is specified as: \\server\folder

ping server
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get the IP-address in format: IIII.JJJJ.KKKK.LLLL

3. Mount manually

sudo mount -t cifs //IP-address/folder /mnt/share \
  -o user=user,password=password,uid=$(id -u),gid=$(id -g),vers=2.1
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set user and password to real username and real password

4. Auto-mount credentials

vim ~/.smbcredentials
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in there:

username=username
password=password
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“secure” it:

chmod 600 ~/.smbcredentials
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5. Auto-mount script

mkdir -p ~/.scripts
vim ~/.scripts/mount-share.sh
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Paste inside:

#!/bin/bash

MOUNTPOINT="/mnt/share"
SHARE="//IP-address/folder"

if ! mountpoint -q "$MOUNTPOINT"; then
  sudo mount -t cifs $SHARE $MOUNTPOINT \
    -o credentials=$HOME/.smbcredentials,uid=$(id -u),gid=$(id -g),vers=2.1
fi
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6. Auto-mount execution when .bashrc is sourced

Make script executable:

chmod +x ~/.scripts/mount-share.sh
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Add to .bashrc

echo "bash ~/.scripts/mount-share.sh &" >> ~/.bashrc
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7. Mount the drive with an automatic log-in

Change the permissions:

sudo visudo
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Add following to the end of the file:

# do an automatic mount of the NAS
<user-name> ALL=(ALL) NOPASSWD: /sbin/mount.cifs, /bin/mount
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