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Diffstat (limited to 'topics/aws/README.gmi')
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diff --git a/topics/aws/README.gmi b/topics/aws/README.gmi new file mode 100644 index 0000000..41981dc --- /dev/null +++ b/topics/aws/README.gmi @@ -0,0 +1,210 @@ +# 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: + +```shell +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: + +```shell +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 + +```shell +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 +``` |