Amazon Web Services

Create a virtual machine

In the browser:

Log in to Amazon Web Services as "Root user" (https://signin.aws.amazon.com/)
Click "Launch a virtual machine"
Select instance's O.S. and type
Create a key pair to securely connect to the instance
Download the created key pair (file `chosen_name.pem`)
Allow HTTPS/HTTP traffic from the internet
Click "Launch instance"

In the local machine:

chmod 400 chosen_name.pem` # ensure your key is not publicly viewable
ssh -i "chosen_name.pem" ubuntu@ec2-54-211-237-62.compute-1.amazonaws.com` # connect to the instance (the address changes every time the machine is restarted)

Note: select the instance and then click 'Instance state' and 'Stop Instance' to stop it.

Create multiple users

In the virtual machine:

ssh -i "chosen_name.pem" ubuntu@ec2-54-211-237-62.compute-1.amazonaws.com # connect to the virtual machine
sudo adduser user1 # create a new user
sudo adduser user2 # create a new user
sudo sed 's/^PasswordAuthentication no/PasswordAuthentication yes/' /etc/ssh/sshd_config -i # allow new users to use SSH with password authentication
sudo systemctl restart sshd # restart the SSH service to apply the changes

Clone a virtual machine

Select the instance
Click "Actions", "Image and templates", and "Create image"
Set "Image name" and click "Create image"
Click Images->"Create AMI in the menu on the left side
Select the AMI and click the "Launch instances from AMI" button

Set up a pangenomic virtual machine

sudo apt-get update
sudo apt-get upgrade
sudo apt-get install -y \
                    git \
                    bash \
                    cmake \
                    make \
                    g++-11 \
                    python3-dev \
                    pybind11-dev \
                    libbz2-dev \
                    bc \
                    libatomic-ops-dev \
                    autoconf \
                    libgsl-dev \
                    zlib1g-dev \
                    libzstd-dev \
                    libjemalloc-dev \
                    libhts-dev \
                    build-essential \
                    pkg-config \
                    time \
                    curl \
                    pigz \
                    tabix \
                    bcftools \
                    samtools \
                    wget \
                    pip \
                    libcairo2-dev \
                    unzip \
                    parallel \
    && sudo apt-get clean \
    && sudo apt-get purge  \
    && sudo rm -rf /var/lib/apt/lists/*
sudo apt-get autoremove

git clone --recursive https://github.com/waveygang/wfmash \
    && cd wfmash \
    && git pull \
    && git checkout 8ba3c53f327731ca515abd1ef32179f15acb9732 \
    && git submodule update --init --recursive \
    && cmake -H. -DCMAKE_BUILD_TYPE=Release -Bbuild && cmake --build build -- -j $(nproc) \
    && sudo cp build/bin/wfmash /usr/local/bin/wfmash \
    && cd ../ \
    && rm -rf wfmash

git clone --recursive https://github.com/ekg/seqwish \
    && cd seqwish \
    && git pull \
    && git checkout d9e7ab59e73258f57875f2a060437735a460475e \
    && git submodule update --init --recursive \
    && cmake -H. -DCMAKE_BUILD_TYPE=Release -Bbuild && cmake --build build -- -j $(nproc) \
    && sudo cp bin/seqwish /usr/local/bin/seqwish \
    && cd ../ \
    && rm -rf seqwish

git clone --recursive https://github.com/pangenome/smoothxg \
    && cd smoothxg \
    && git pull \
    && git checkout 956eb75644522bb2b96b4cca44b7bafa9cf02f4a \
    && git submodule update --init --recursive \
    && cmake -H. -DCMAKE_BUILD_TYPE=Release -Bbuild && cmake --build build -- -j $(nproc) \
    && sudo cp bin/smoothxg /usr/local/bin/smoothxg \
    && sudo cp deps/odgi/bin/odgi /usr/local/bin/odgi \
    && cd ../ \
    && rm -rf odgi

curl https://sh.rustup.rs -sSf | sh -s -- -y
PATH="$HOME/.cargo/bin:${PATH}"

git clone https://github.com/marschall-lab/GFAffix.git \
    && cd GFAffix \
    && git pull \
    && git checkout 3784c7ee03ee82df576474d2e119fdd88616914b \
    && cargo install --force --path . \
    && sudo mv $HOME/.cargo/bin/gfaffix /usr/local/bin/gfaffix \
    && cd ../ \
    && rm -rf GFAffix


wget https://github.com/vgteam/vg/releases/download/v1.40.0/vg \
    && chmod +x vg \
    && sudo mv vg /usr/local/bin/vg

git clone https://github.com/pangenome/vcfbub \
    && cd vcfbub \
    && git pull \
    && git checkout 26a1f0cb216a423f8547c4ad0e0ce38cb9d324b9 \
    && cargo install --force --path . \
    && sudo mv $HOME/.cargo/bin/vcfbub /usr/local/bin/vcfbub \
    && cd ../ \
    && rm -rf vcfbub

git clone --recursive https://github.com/vcflib/vcflib.git \
    && cd vcflib \
    && git checkout 4f2bce873bc520449ec549f36aaaad65bace51ca \
    && mkdir -p build \
    && cd build \
    && cmake -DZIG=OFF -DCMAKE_BUILD_TYPE=Release .. && cmake --build . -- -j $(nproc) \
    && sudo mv vcfwave /usr/local/bin/vcfwave \
    && sudo mv vcfuniq /usr/local/bin/vcfuniq \
    && cd ../../ \
    && rm -rf vcflib

git clone https://github.com/ekg/fastix.git \
    && cd fastix \
    && git pull \
    && git checkout 331c1159ea16625ee79d1a82522e800c99206834 \
    && cargo install --force --path . \
    && sudo mv $HOME/.cargo/bin/fastix /usr/local/bin/fastix \
    && cd ../ \
    && rm -rf fastix

git clone https://github.com/ekg/pafplot.git \
    && cd pafplot \
    && git pull \
    && git checkout 7dda24c0aeba8556b600d53d748ae3103ec85501 \
    && cargo install --force --path . \
    && sudo mv $HOME/.cargo/bin/pafplot /usr/local/bin/ \
    && cd ../ \
    && rm -rf pafplot

pip install igraph==0.10.4
pip install pycairo==1.23.0
pip install multiqc==1.14
sudo mv /home/ubuntu/.local/bin/* /usr/local/bin/

git clone https://github.com/pangenome/pggb.git
cd pggb
git checkout de5303e24d3e5594a5a2c9bdeb49aba420b24b0c
sudo cp pggb /usr/local/bin/pggb
sudo chmod 777 /usr/local/bin/pggb
sudo cp partition-before-pggb /usr/local/bin/partition-before-pggb
sudo chmod 777 /usr/local/bin/partition-before-pggb
sudo cp scripts/* /usr/local/bin/ # copy required scripts

# Hacky-way to easily get versioning info
sudo cp -r .git /usr/local/bin/
git config --global --add safe.directory /usr/local/bin
cd ..
rm -rf pggb

# Docker (for Nextflow)
sudo apt-get remove docker docker-engine docker.io
sudo apt-get update
sudo apt install docker.io
sudo snap install docker
sudo groupadd docker # create the docker group
sudo usermod -aG docker ${USER} # add yourself to the docker group
#  log out and log back in so that your group membership is re-evaluated
docker run hello-world # test it
# reboot the instance

# Java 17 (for Nextflow)
sudo apt install openjdk-17-jre-headless

# Nextflow
wget -qO- https://get.nextflow.io | bash
sudo cp nextflow /usr/local/bin/nextflow
sudo chmod 777 /usr/local/bin/nextflow
nextflow run nf-core/pangenome -r a_brave_new_world -profile test,docker --outdir a_brave_new_world.output # test it
nextflow run nf-core/pangenome -r a_brave_new_world --input pggb/data/HLA/DRB1-3123.fa.gz --n_haplotypes 14 --outdir uffa -profile docker -c hla.config # to ask for less resources