Created
December 5, 2025 10:00
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Oncoanalyser dev setup on AWS AmazonLinux 2023 (for Aarch64 support development)
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| sudo yum -y install git java-23-amazon-corretto-devel java-23-amazon-corretto tmux htop gcc g++ gdb zlib-devel zlib wget patch pigz | |
| cd /opt && sudo wget https://services.gradle.org/distributions/gradle-8.13-bin.zip && sudo unzip gradle-8.13-bin.zip && sudo rm gradle-8.13-bin.zip && sudo ln -sf /opt/gradle-8.13/ /opt/gradle && export PATH=$PATH:/opt/gradle/bin && cd $HOME | |
| wget https://github.com/aristocratos/btop/releases/download/v1.4.0/btop-`uname -i`-linux-musl.tbz && tar xvfj btop-`uname -i`-linux-musl.tbz && sudo mv btop/bin/btop /usr/local/bin && rm -rf btop* | |
| wget https://kojipkgs.fedoraproject.org//packages/pbzip2/1.1.13/1.el8/`uname -i`/pbzip2-1.1.13-1.el8.`uname -i`.rpm && sudo rpm -i *.rpm && rm *.rpm | |
| git clone https://github.com/nf-core/oncoanalyser && cd oncoanalyser && git checkout dev | |
| curl -s https://get.nextflow.io | bash | |
| chmod +x nextflow && sudo mv nextflow /usr/local/bin | |
| mkdir -p ~/miniconda3 | |
| wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-`uname -i`.sh -O ~/miniconda3/miniconda.sh | |
| bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3 | |
| rm ~/miniconda3/miniconda.sh | |
| source ~/miniconda3/bin/activate | |
| conda init --all | |
| # ----- cut here for instance userscript ----- # | |
| # Interactive dev usage follows | |
| tmux | |
| conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/main | |
| conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/r | |
| nextflow run . -resume -profile conda,test --outdir ../testrun-output-pipeline_v6.0_`uname -i` |
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