Run as biocbuild, consolidate startup scripts

Dockerfile

@@ -2,14 +2,16 @@ ARG BASE_IMAGE=ubuntu:noble
 FROM ${BASE_IMAGE} AS build
 ARG CYCLE=release
 ARG NAME=
-RUN useradd -ms /bin/bash biocbuild && apt update -qq && apt install sudo systemd -y && usermod -aG sudo biocbuild && echo "biocbuild ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
+RUN useradd -m -s /bin/bash -u 1007 biocbuild && apt update -qq && apt install sudo systemd -y && usermod -aG sudo biocbuild && echo "biocbuild ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
 USER biocbuild
 COPY . /home/biocbuild/bioconductor_salt
 WORKDIR /home/biocbuild
-RUN DEBIAN_FRONTEND="noninteractive" bash bioconductor_salt/startup_bbs_standalone_${CYCLE}.sh ${NAME}
+RUN DEBIAN_FRONTEND="noninteractive" bash bioconductor_salt/startup_bbs_standalone.sh ${CYCLE} ${NAME}
 
 FROM ${BASE_IMAGE} AS final
 COPY --from=build / /
+USER biocbuild
+WORKDIR /home/biocbuild
 ENTRYPOINT ["/bin/bash", "-c"]
 CMD ["/bbs_r_start"]
 

saltstack/pillar/common/linux.sls

@@ -1,6 +1,7 @@
 build:
   types:
     - bioc                  {# always required #}
+    - bioc-gpu
     - bioc-longtests
     - books
     - data-annotation

saltstack/salt/common/linux.sls

@@ -101,6 +101,7 @@ install_pkgs_for_gpu:
       - texlive-fonts-extra
       - libthrust-dev
       - libcub-dev
+      - rsync
 {% else %}
 install_apt_pkgs:
   cmd.run:

startup_bbs_standalone_devel.sh → startup_bbs_standalone.sh

@@ -26,13 +26,19 @@ 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
 
-if [ "${1}" = "nvidia-noble" ]; then
+if [ "${1}" = "devel" ]; then
+	cycle="devel"
+else
+	cycle="release"
+fi
+
+if [ "${2}" = "nvidia-noble" ]; then
 	opt="_gpu"
 else
 	opt=""
 fi
 
-sudo mv /srv/pillar/custom/devel_standalone${opt}.sls /srv/pillar/custom/init.sls
+sudo mv /srv/pillar/custom/${cycle}_standalone${opt}.sls /srv/pillar/custom/init.sls
 
 sudo salt-call --local state.highstate || true
 
@@ -47,6 +53,9 @@ sudo echo "export PATH='$PATH:$RPATH'" | sudo tee -a /etc/bash.bashrc
 sudo echo "#!/bin/bash" | sudo tee /bbs_r_start
 sudo echo "$RPATH/R \"\$@\"" | sudo tee -a /bbs_r_start
 
+# Change permissions for volumes
+sudo echo "sudo chown -R biocbuild:biocbuild /home/biocbuild" | sudo tee -a /bbs_r_start
+
 sudo chown biocbuild /bbs_r_start
 sudo chmod +x /bbs_r_start