From 2fc42be0fc41c1d565789adeb8fc3aefb2e54027 Mon Sep 17 00:00:00 2001
From: J Wokaty <jwokaty@users.noreply.github.com>
Date: Thu, 23 Jan 2025 19:26:18 -0500
Subject: [PATCH] Add sudo back to devel script

---
 startup_bbs_standalone_devel.sh | 44 ++++++++++++++++-----------------
 1 file changed, 22 insertions(+), 22 deletions(-)

diff --git a/startup_bbs_standalone_devel.sh b/startup_bbs_standalone_devel.sh
index 2e5e63f..9318b6b 100644
--- a/startup_bbs_standalone_devel.sh
+++ b/startup_bbs_standalone_devel.sh
@@ -1,54 +1,54 @@
 #!/usr/bin/env bash
 
 # Basic deps
-apt update -qq
-apt -y install curl git build-essential python3 python3-pip locales wget
+sudo apt update -qq
+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/linux-deb.html
 
 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
+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
 
-apt-get -y update
-apt-get -y install salt-minion
-service salt-minion stop
-systemctl disable salt-minion
+sudo apt-get -y update
+sudo apt-get -y install salt-minion
+sudo service salt-minion stop
+sudo 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
-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 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
 
-mv /srv/pillar/custom/devel_standalone.sls /srv/pillar/custom/init.sls
+sudo mv /srv/pillar/custom/devel_standalone.sls /srv/pillar/custom/init.sls
 
-salt-call --local state.highstate || true
+sudo 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'" | tee -a /etc/profile
-echo "export PATH='$PATH:$RPATH'" | tee -a /etc/bash.bashrc
+sudo echo "export PATH='$PATH:$RPATH'" | sudo tee -a /etc/profile
+sudo echo "export PATH='$PATH:$RPATH'" | sudo tee -a /etc/bash.bashrc
 
-echo "#!/bin/bash" | tee /bbs_r_start
-echo "$RPATH/R \"\$@\"" | tee -a /bbs_r_start
+sudo echo "#!/bin/bash" | sudo tee /bbs_r_start
+sudo echo "$RPATH/R \"\$@\"" | sudo tee -a /bbs_r_start
 
-chown biocbuild /bbs_r_start
-chmod +x /bbs_r_start
+sudo chown biocbuild /bbs_r_start
+sudo chmod +x /bbs_r_start
 
-ln -s /home/biocbuild/bbs-*-bioc/R/bin/R /usr/bin/R
-ln -s /home/biocbuild/bbs-*-bioc/R/bin/Rscript /usr/bin/Rscript
+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
 
 # Cleanup
 # rm -rf /srv /etc/salt
-# apt-get -y purge salt-minion
+# sudo apt-get -y purge salt-minion