diff --git a/startup_bbs_standalone_devel.sh b/startup_bbs_standalone_devel.sh index c53d633..2e5e63f 100644 --- a/startup_bbs_standalone_devel.sh +++ b/startup_bbs_standalone_devel.sh @@ -1,53 +1,54 @@ #!/usr/bin/env bash # Basic deps -sudo apt update -qq -sudo apt -y install curl git build-essential python3 python3-pip locales wget +apt update -qq +apt -y install curl git build-essential python3 python3-pip locales wget # Set up saltstack -# https://docs.saltproject.io/salt/install-guide/en/latest/topics/install-by-operating-system/ubuntu.html +#https://docs.saltproject.io/salt/install-guide/en/latest/topics/install-by-operating-system/linux-deb.html -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 +mkdir -p /etc/apt/keyrings +curl -fsSL https://packages.broadcom.com/artifactory/api/security/keypair/SaltProjectKey/public | tee /etc/apt/keyrings/salt-archive-keyring.pgp +curl -fsSL https://github.com/saltstack/salt-install-guide/releases/latest/download/salt.sources | tee /etc/apt/sources.list.d/salt.sources -sudo apt-get -y update -sudo apt-get -y install salt-minion -sudo service salt-minion stop -sudo systemctl disable salt-minion +apt-get -y update +apt-get -y install salt-minion +service salt-minion stop +systemctl disable salt-minion # Assumes the repository has already been cloned to the working directory # cd ~ # git clone -b standalone https://github.com/Bioconductor/bioconductor_salt # 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 +cp -r bioconductor_salt/saltstack/salt /srv +cp -r bioconductor_salt/saltstack/pillar /srv +cp bioconductor_salt/saltstack/minion.d/minion.conf /etc/salt/minion -sudo mv /srv/pillar/custom/devel_standalone.sls /srv/pillar/custom/init.sls +mv /srv/pillar/custom/devel_standalone.sls /srv/pillar/custom/init.sls -sudo salt-call --local state.highstate || true +salt-call --local state.highstate || true # Find R path and check that it works if ! /home/biocbuild/bbs-*/R/bin/R --version > /tmp/rver; then exit 1; fi RPATH="$(echo /home/biocbuild/bbs-*/R/bin)" -echo "export PATH='$PATH:$RPATH'" | sudo tee -a /etc/profile -echo "export PATH='$PATH:$RPATH'" | sudo tee -a /etc/bash.bashrc +echo "export PATH='$PATH:$RPATH'" | tee -a /etc/profile +echo "export PATH='$PATH:$RPATH'" | tee -a /etc/bash.bashrc -echo "#!/bin/bash" | sudo tee /bbs_r_start -echo "$RPATH/R \"\$@\"" | sudo tee -a /bbs_r_start +echo "#!/bin/bash" | tee /bbs_r_start +echo "$RPATH/R \"\$@\"" | tee -a /bbs_r_start -sudo chown biocbuild /bbs_r_start -sudo chmod +x /bbs_r_start +chown biocbuild /bbs_r_start +chmod +x /bbs_r_start -sudo ln -s /home/biocbuild/bbs-*-bioc/R/bin/R /usr/bin/R -sudo ln -s /home/biocbuild/bbs-*-bioc/R/bin/Rscript /usr/bin/Rscript +ln -s /home/biocbuild/bbs-*-bioc/R/bin/R /usr/bin/R +ln -s /home/biocbuild/bbs-*-bioc/R/bin/Rscript /usr/bin/Rscript # Cleanup # rm -rf /srv /etc/salt -# sudo apt-get -y purge salt-minion +# apt-get -y purge salt-minion diff --git a/startup_bbs_standalone_release.sh b/startup_bbs_standalone_release.sh index a6e08e4..6afacf5 100644 --- a/startup_bbs_standalone_release.sh +++ b/startup_bbs_standalone_release.sh @@ -6,10 +6,11 @@ sudo apt -y install curl git build-essential python3 python3-pip locales wget # Set up saltstack -# https://docs.saltproject.io/salt/install-guide/en/latest/topics/install-by-operating-system/ubuntu.html +#https://docs.saltproject.io/salt/install-guide/en/latest/topics/install-by-operating-system/linux-deb.html -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 +mkdir -p /etc/apt/keyrings +curl -fsSL https://packages.broadcom.com/artifactory/api/security/keypair/SaltProjectKey/public | sudo tee /etc/apt/keyrings/salt-archive-keyring.pgp +curl -fsSL https://github.com/saltstack/salt-install-guide/releases/latest/download/salt.sources | sudo tee /etc/apt/sources.list.d/salt.sources sudo apt-get -y update sudo apt-get -y install salt-minion