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Add RStudio 2026.09.0-174 (R 4.6.1) and libwebp-dev to the recipe #192

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Merged
kennedydane merged 3 commits into from
Sep 23, 2026
Merged

Add RStudio 2026.09.0-174 (R 4.6.1) and libwebp-dev to the recipe #192

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2e6ea00
Add libwebp-dev to the RStudio recipe
kennedydane Sep 23, 2026
bb6fcbb
Add RStudio 2026.09.0-174 with R 4.6.1 on Ubuntu noble
kennedydane Sep 23, 2026
9be1a85
Make the SSH jump host in container instructions configurable
kennedydane Sep 23, 2026
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4 changes: 4 additions & 0 deletions ansible/group_vars/all
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Expand Up @@ -52,6 +52,10 @@ common_modules: "{{ modules_dir }}/common"

admin_group: "idia-admins"

# SSH jump host printed in the connection instructions of interactive containers
# (RStudio, PopGen). Override with -e login_host=... or in the inventory.
login_host: "slurm.ilifu.ac.za"

# 4.4.1 is built --without-suid (see roles/compiled/tasks/common/singularity.yaml);
# 4.1.0 still ships a setuid starter-suid. Note 4.4.2 is registered in
# roles/compiled/tasks/common/main.yml but is not yet installed on /software.
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5 changes: 5 additions & 0 deletions ansible/roles/containers/tasks/common/main.yml
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Expand Up @@ -34,6 +34,11 @@
rstudio_deb_release: jammy
r_version: 4.6.1
rstudio_version: 2026.07.1-147
- base_container_name: ubuntu-noble-compile
base_container_version_name: noble
rstudio_deb_release: jammy
r_version: 4.6.1
rstudio_version: 2026.09.0-174
ansible.builtin.include_tasks:
file: RStudio.yaml
loop: "{{ rstudio_versions }}"
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4 changes: 2 additions & 2 deletions ansible/roles/containers/templates/bio/PopGen.def
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Expand Up @@ -23,7 +23,7 @@ From: {{ base_container_image }}
HOST=$( /bin/hostname )
echo "Running rserver on port ${PORT}"
echo "To connect to this server run this on your local machine:"
echo " ssh -A ${USER}@${HOST} -o \"ProxyCommand=ssh ${USER}@slurm.ilifu.ac.za nc ${HOST} 22\" -L8081:localhost:${PORT}"
echo " ssh -A ${USER}@${HOST} -o \"ProxyCommand=ssh ${USER}@{{ login_host }} nc ${HOST} 22\" -L8081:localhost:${PORT}"
echo "then vist http://localhost:8081 in your browser and use the username \"${USER}\" to login with the password \"${RSTUDIO_PASSWORD}\""
echo "(You may need to choose a different port (other than 8081), so remember to change this in both the ssh and browser)"
exec rserver --auth-none 0 --auth-pam-helper rstudio_auth --secure-cookie-key-file /tmp/rstudio-server-${USER}/secure-cookie.key --www-port ${PORT} "${@}"
Expand Down Expand Up @@ -70,7 +70,7 @@ From: {{ base_container_image }}
HOST=$( /bin/hostname )
echo "Running rserver on port ${PORT}"
echo "To connect to this server run this on your local machine:"
echo " ssh -A ${USER}@${HOST} -o \"ProxyCommand=ssh ${USER}@slurm.ilifu.ac.za nc ${HOST} 22\" -L8081:localhost:${PORT}"
echo " ssh -A ${USER}@${HOST} -o \"ProxyCommand=ssh ${USER}@{{ login_host }} nc ${HOST} 22\" -L8081:localhost:${PORT}"
echo "then vist http://localhost:8081 in your browser and use the username \"${USER}\" to login with the password \"${RSTUDIO_PASSWORD}\""
echo "(You may need to choose a different port (other than 8081), so remember to change this in both the ssh and browser)"
exec rserver --auth-none 0 --auth-pam-helper rstudio_auth --secure-cookie-key-file /tmp/rstudio-server-${USER}/secure-cookie.key --www-port ${PORT} "${@}"
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5 changes: 3 additions & 2 deletions ansible/roles/containers/templates/common/RStudio.def
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Expand Up @@ -24,7 +24,7 @@ From: {{ base_container_image }}
HOST=$( /bin/hostname )
echo "Running rserver on port ${PORT}"
echo "To connect to this server run this on your local machine:"
echo " ssh -A ${USER}@${HOST} -o \"ProxyCommand=ssh ${USER}@slurm.ilifu.ac.za nc ${HOST} 22\" -L8081:localhost:${PORT}"
echo " ssh -A ${USER}@${HOST} -o \"ProxyCommand=ssh ${USER}@{{ login_host }} nc ${HOST} 22\" -L8081:localhost:${PORT}"
echo "then visit http://localhost:8081 in your browser and use the username \"${USER}\" to login with the password \"${RSTUDIO_PASSWORD}\""
echo "(You may need to choose a different port (other than 8081), so remember to change this in both the ssh and browser)"
exec rserver --server-user ${USER} --auth-none 0 --auth-pam-helper rstudio_auth --secure-cookie-key-file ${HOME}/.RStudio.rserver/secure-cookie.key --www-port ${PORT} --server-data-dir ${HOME}/.RStudio.rserver/data "${@}"
Expand All @@ -38,7 +38,7 @@ From: {{ base_container_image }}
HOST=$( /bin/hostname )
echo "Running rserver on port ${PORT}"
echo "To connect to this server run this on your local machine:"
echo " ssh -A ${USER}@${HOST} -o \"ProxyCommand=ssh ${USER}@slurm.ilifu.ac.za nc ${HOST} 22\" -L8081:localhost:${PORT}"
echo " ssh -A ${USER}@${HOST} -o \"ProxyCommand=ssh ${USER}@{{ login_host }} nc ${HOST} 22\" -L8081:localhost:${PORT}"
echo "then visit http://localhost:8081 in your browser and use the username \"${USER}\" to login with the password \"${RSTUDIO_PASSWORD}\""
echo "(You may need to choose a different port (other than 8081), so remember to change this in both the ssh and browser)"
exec rserver --server-user ${USER} --auth-none 0 --auth-pam-helper rstudio_auth --secure-cookie-key-file ${HOME}/.RStudio.rserver/secure-cookie.key --www-port ${PORT} --server-data-dir ${HOME}/.RStudio.rserver/data "${@}"
Expand Down Expand Up @@ -118,6 +118,7 @@ From: {{ base_container_image }}
libssl-dev \
libtiff5-dev \
libuv1-dev \
libwebp-dev \
libxml2-dev \
libxt-dev \
netcdf-bin \
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