Salt to Configure a Linux or Mac for the BBS

This repository contains the SaltStack formulas to configure an Ubuntu or a MacOS machine for the Bioconductor Build System.

It also builds BBS-like containers.

Simulating the BBS Ubuntu environment in a container

We are building and publishing containers under the name ghcr.io/bioconductor/bioconductor_salt, which can be used to mimic a BBS-like linux environment, in hopes of easing reproducibility and interactive debugging of the BBS environment for package developers.

We currently offer containers for both release and devel Bioconductor versions with Ubuntu noble (24.04). Container tags with various version pinnings can be used to acquire a particular environment, following the schema [ubuntu_version]-bioc-[bioc_version]-r-[r_version] eg noble-bioc-3.22-r-4.5.0 or 24.04-bioc-3.22-r-4.5.0, where each level is optional. For example, one could use tag noble-bioc-3.22or24.04-bioc-3.22to get the latest 3.22, regardless of R version, or even simplynoble/24.04to get the latest release container.devel-` will prefix all devel container tags, followed by the same schema described above.

All containers will use the R command if no command is specified. Below are some examples for running the container.

# Interactive R session
docker run -it ghcr.io/bioconductor/bioconductor_salt:noble
# is equivalent to
docker run -it ghcr.io/bioconductor/bioconductor_salt:noble R

# Bash shell
docker run -it ghcr.io/bioconductor/bioconductor_salt:noble bash

# Rscript
docker run -it ghcr.io/bioconductor/bioconductor_salt:noble "Rscript --version"

We are also experimentally building BBS-like containers based on Nvidia containers, which can be run as

docker run --gpus all -it ghcr.io/bioconductor/bioconductor_salt:devel-nvidia-noble R

Note for containers with an Nvidia base

This software contains source code provided by NVIDIA Corporation.

These containers are subject to https://developer.download.nvidia.com/licenses/NVIDIA_Deep_Learning_Container_License.pdf.

Configuring for Ubuntu 24.04

1. On the build machine, install the Salt minion and clone this repository:

   sudo apt install salt-minion
   

Note: If the minion is running as a daemon, you'll want to stop it as it will poll for the master periodically.

2. Copy saltstack/minion.d/minion.conf to /etc/salt/minion.

3. Copy the files in /saltstack to /srv.

4. Copy ssh keys to /srv/salt/common/files.

5. Comment add or remove any dependencies not needed for your system in /opt/salt/top.sls.

6. Run salt, with debug or testing (test=True) if desired:

   sudo salt-call --local state.highstate -l debug
   

7. Configure the BBS configuration files.

8. Uncomment the desired builds in the crontab as biocbuild.

Configuring a Mac

1. On the build machine, install Saltstack by downloading the file corresponding to your OS at https://docs.saltproject.io/salt/install-guide/en/latest/topics/install-by-operating-system/macos.html.

For example

```
curl -LO https://repo.saltproject.io/salt/py3/macos/latest/salt-3007.0-py3-x86_64.pkg
sudo installer -verbose -pkg salt-3007.0-py3-x86_64.pkg -target /
```

Log out and log back in then check if salt-call is available with which salt-call.

2. Copy saltstack/minion.d/mac.minion.conf to /etc/salt/minion.

3. Copy saltstack to /opt.

4. Copy ssh keys to /opt/saltstack/salt/common/files.

5. Comment add or remove any dependencies not needed for your system in /opt/saltstack/salt/top.sls.

6. If creating user biocbuild, set the password in an environment variable:

   export BIOCBUILD_PASSWORD=myNewPass1

7. Run salt, with debug or testing (test=True) if desired:

   sudo salt-call --local state.highstate -l debug
   

8. Configure the BBS configuration files.

9. Uncomment the desired builds in the crontab as biocbuild.

Updating R

Note: If macFuse is needed and it will be installed on the machine for the first time, you may need to enable kernel support for third party extensions. See https://github.com/macfuse/macfuse/wiki/Getting-Started.

You may also run individual states, such as to update R. After configuring the custom file for your machine, run the rlang states for your machine.

Replace the url for r_download with the new version of R in saltstack/pillar/custom/init.sls:

{% set branch = 'dev' %} {# Use 'release' or 'devel' #}
{% set version = '3.15' %}
{% set environment = 'dev' %} {# Use 'dev' or 'prod' #}
{% set r_download = 'https://stat.ethz.ch/R/daily/R-devel_2021-11-16.tar.gz' %}
{% set r_version = 'R-4.1.2' %}
{% set cycle = 'patch' %} {# Use 'devel' for Spring to Fall, 'patch' for Fall to Spring #}

Update any related variables, such as r_version. To perform the update, run

sudo salt-call --local state.apply rlang.linux

Standalone Machine with BBS dependencies

If machine_type equals standalone in pillar/custom/init.sls, the machine will be configured with the dependencies needed for the build system but without the set up necessary to perform the official builds. A standalone build might be sufficient for testing R CMD INSTALL build or check. It will also reduce the time necessary for configuration.