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makeing_machines.md

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Making machines for the workshops

We usually use Google Cloud, AWS or Nectar

  • When booting a new machine, make sure that you allow SSH access in the security groups. It needs a group that provides port 22 access to all IP address (0.0.0.0/0)
  • Make sure you add additional space for user accounts, usually as an external volume:
    • mount the volume in the web server (e.g. as /dev/vdb1)
    • use fdisk /dev/vdb to make a new partition
    • use mkfs.ext4 /dev/vdb1 to format that
    • mount it on /storage: mkdir /storage && mount /dev/vdb1 /storage
  • make user and data directories: mkdir /storage/users/ /storage/data
  • set the ubuntu password so you can enable passwords: sudo passwd ubuntu
  • enable passwords:
sudo vi /etc/ssh/sshd_config
# Change PasswordAuthentication no to yes.
# Save and exit
sudo /etc/init.d/sshd reload

# for debian use
service sshd reload

# while you are at it:

apt update && apt install build-essential && apt -y dist-upgrade
  • create the users with create_newusers.py. Note that this version sets their home directory to /storage/users/$USER
python ~/GitHubs/EdwardsLab/bin/create_newusers.py -m storage/users -n 200 -s 5
  • copy these files across to the ubuntu machine and use newusers to setup the accounts:
scp -i ~/.ssh/xxxxxxxxxxxxx_rsa users.tsv accounts.tsv [email protected]:
# login to the host
sudo newusers users.tsv
  • check the you can log in with e.g. user number 100.

Installing pony

We are trying pony linux

install software

  • install git/texinfo: apt-get update && apt-get install -y git texinfo
  • install ponysay:
cd /root
git clone https://github.com/erkin/ponysay.git
cd ponysay/
python3 setup.py --freedom=partial install

Now install PonyLinux somewhere everyone can use it:

cd /storage
mkdir git
cd git
git clone https://github.com/NCGAS/PonyLinux.git

Next, link this to each users home directory:

cd /storage/users/
for USER in user*; do ln -s /storage/git/PonyLinux $USER/PonyLinux; chown $USER:$USER $USER/PonyLinux; done

Now when they log in, they can cd PonyLinux; ./PonyLinux.sh

Install bioconda

Download miniforge:

curl -LO https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
bash  Miniforge3-Linux-x86_64.sh

Make a ~/.bash_profile file

vi bash_profile

Paste this text:

if [ -f ~/.bashrc ]; then    
	. ~/.bashrc
fi

Then copy to all users:

for USER in user0*; do cp bash_profile $USER/.bash_profile; chown $USER:$USER $USER/.bash_profile; done

Install binchicken and download databases

mamba create -n binchicken -y -c bioconda -c conda-forge "binchicken>=0.12.5"

mamba activate binchicken
binchicken build  --conda-prefix miniforge3  --singlem-metapackage metapackage --checkm2-db checkm2 --download-databases