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Add release/devel cycle and Bioc version in tag (#126)
* Add release/devel cycle and Bioc version in tag * Renaming cycle to branch * Change cycle to patch * Change devel tarball
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,8 +1,9 @@ | ||
| FROM ubuntu:jammy | ||
| ARG CYCLE=release | ||
| RUN useradd -ms /bin/bash biocbuild && apt update -qq && apt install sudo systemd -y && usermod -aG sudo biocbuild && echo "biocbuild ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers | ||
| USER biocbuild | ||
| COPY . /home/biocbuild/bioconductor_salt | ||
| WORKDIR /home/biocbuild | ||
| RUN bash bioconductor_salt/simple_start_linux.sh | ||
| RUN bash bioconductor_salt/startup_bbs_standalone_${CYCLE}.sh | ||
| ENTRYPOINT ["/bbs_r_start"] | ||
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| @@ -0,0 +1,13 @@ | ||
| {# Custom Settings #} | ||
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| {% set branch = 'devel' %} {# Use 'release' or 'devel' #} | ||
| {% set version = '3.19' %} | ||
| {% set environment = 'dev' %} {# Use 'dev' or 'prod' #} | ||
| {% set r_download = 'https://stat.ethz.ch/R/daily/R-devel.tar.gz' %} | ||
| {% set r_version = 'R-4.4' %} | ||
| {% set r_previous_version = 'R-4.3' %} | ||
| {% set cycle = 'patch' %} {# Use 'devel' for Spring to Fall, 'patch' for Fall to Spring #} | ||
| {% set name = 'bbs-machine' %} | ||
| {% set immunespace_pwd = '' %} | ||
| {% set create_users = False %} | ||
| {% set machine_type = 'standalone' %} |
6 changes: 3 additions & 3 deletions
6
saltstack/pillar/custom/standalone.sls → ...tack/pillar/custom/release_standalone.sls
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,51 @@ | ||
| #!/usr/bin/env bash | ||
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| # Basic deps | ||
| sudo apt update -qq | ||
| sudo apt -y install curl git build-essential python3 python3-pip locales wget | ||
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| # Set up saltstack | ||
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| # https://docs.saltproject.io/salt/install-guide/en/latest/topics/install-by-operating-system/ubuntu.html | ||
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| sudo curl -fsSL -o /etc/apt/keyrings/salt-archive-keyring-2023.gpg https://repo.saltproject.io/salt/py3/ubuntu/22.04/amd64/SALT-PROJECT-GPG-PUBKEY-2023.gpg | ||
| echo "deb [signed-by=/etc/apt/keyrings/salt-archive-keyring-2023.gpg arch=amd64] https://repo.saltproject.io/salt/py3/ubuntu/22.04/amd64/latest jammy main" | sudo tee /etc/apt/sources.list.d/salt.list | ||
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| sudo apt-get -y update | ||
| sudo apt-get -y install salt-minion | ||
| sudo service salt-minion stop | ||
| sudo systemctl disable salt-minion | ||
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| # Assumes the repository has already been cloned to the working directory | ||
| # cd ~ | ||
| # git clone -b standalone https://github.com/Bioconductor/bioconductor_salt | ||
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| # Set up bioconductor's saltstack | ||
| sudo cp -r bioconductor_salt/saltstack/salt /srv | ||
| sudo cp -r bioconductor_salt/saltstack/pillar /srv | ||
| sudo cp bioconductor_salt/saltstack/minion.d/minion.conf /etc/salt/minion | ||
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| sudo mv /srv/pillar/custom/release_standalone.sls /srv/pillar/custom/init.sls | ||
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| sudo salt-call --local state.highstate -l debug || true | ||
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| # Find R path and check that it works | ||
| /home/biocbuild/bbs-*/R/bin/R --version > /tmp/rver | ||
| if ! grep -q 'R version' /tmp/rver; then exit 1; fi | ||
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| RPATH="$(echo /home/biocbuild/bbs-*/R/bin)" | ||
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| echo "export PATH='$PATH:$RPATH'" | sudo tee -a /etc/profile | ||
| echo "export PATH='$PATH:$RPATH'" | sudo tee -a /etc/bash.bashrc | ||
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| echo "#!/bin/bash" | sudo tee /bbs_r_start | ||
| echo "$RPATH/R \"\$@\"" | sudo tee -a /bbs_r_start | ||
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| sudo chown biocbuild /bbs_r_start | ||
| sudo chmod +x /bbs_r_start | ||
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| # Cleanup | ||
| # rm -rf /srv /etc/salt | ||
| # sudo apt-get -y purge salt-minion | ||
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