an instance of the Orchestrating Spatial Transcriptomics Analysis book
Jun 8 2026: use us.gcr.io/broad-dsp-gcr-public/terra-base:1.0.1 to have sudo capabilities.
To install the infrastructure, et a machine with 4 CPUs and 150 GB disk.
We use r2u to get packages and ubuntu infrastructure. Specifically, we use the script
#!/bin/bash
## See the README.md of 'r2u' for details on these steps
##
## This script has been tested on a plain and minimal ubuntu:22.04
##
## On a well-connected machine this script should take well under one minute
##
## Note that you need to run this as root
## First: update apt and get keys
apt update -qq && apt install --yes --no-install-recommends wget ca-certificates gnupg
wget -q -O- https://eddelbuettel.github.io/r2u/assets/dirk_eddelbuettel_key.asc \
| tee -a /etc/apt/trusted.gpg.d/cranapt_key.asc
## Second: add the repo -- here we use the well-connected mirror
echo "deb [arch=amd64] https://r2u.stat.illinois.edu/ubuntu jammy main" > /etc/apt/sources.list.d/cranapt.list
apt update
## Third: ensure current R is used
wget -q -O- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc \
| tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
echo "deb [arch=amd64] https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/" > /etc/apt/sources.list.d/cran_r.list
apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 67C2D66C4B1D4339 51716619E084DAB9
apt update -qq
DEBIAN_FRONTEND=noninteractive apt install --yes --no-install-recommends r-base-core
## Fourth: add pinning to ensure package sorting
echo "Package: *" > /etc/apt/preferences.d/99cranapt
echo "Pin: release o=CRAN-Apt Project" >> /etc/apt/preferences.d/99cranapt
echo "Pin: release l=CRAN-Apt Packages" >> /etc/apt/preferences.d/99cranapt
echo "Pin-Priority: 700" >> /etc/apt/preferences.d/99cranapt
## Fifth: install bspm (and its Python requirements) and enable it
## If needed (in bare container, say) install python tools for bspm and R itself
apt install --yes --no-install-recommends python3-{dbus,gi,apt} make
## Then install bspm (as root) and enable it, and enable a speed optimization
Rscript -e 'install.packages("bspm")'
RHOME=$(R RHOME)
echo "suppressMessages(bspm::enable())" >> ${RHOME}/etc/Rprofile.site
echo "options(bspm.version.check=FALSE)" >> ${RHOME}/etc/Rprofile.site
We benefit from
sudo mkdir -p /run/dbus
dbus-daemon --system --fork
One r2u is functioning, these steps acquire the OSTA book dependencies:
install.packages("BiocManager")
BiocManager::install(c('anndataR', 'AUCell', 'Banksy', 'basilisk', 'BayesSpace', 'BiocFileCache',
'BiocParallel', 'CARDspa', 'DESpace', 'doMC', 'dplyr', 'DropletUtils', 'EBImage', 'ExperimentHub',
'GenomeInfoDb', 'ggfortify', 'ggplot2', 'ggrepel', 'ggspavis', 'harmony', 'hoodscanR', 'igraph',
'imcdatasets', 'imcRtools', 'jsonlite', 'lme4', 'lmerTest', 'msigdbr', 'muSpaData', 'nnSVG', 'openxlsx',
'osfr', 'OSTA.data', 'pals', 'patchwork', 'pheatmap', 'RANN', 'RColorBrewer', 'reticulate', 'rtracklayer',
'scales', 'scater', 'scider', 'scran', 'scuttle', 'scRNAseq', 'sf', 'SFEData', 'SingleR', 'sosta', 'SpaceTrooper',
'spacexr', 'SpatialExperiment', 'SpatialExperimentIO', 'spatialFDA', 'SpatialFeatureExperiment',
'spatialLIBD', 'spatstat', 'spdep', 'spicyR', 'SpotSweeper', 'STexampleData', 'tidyr',
'VisiumIO', 'Voyager', 'zoo'), Ncpus=3)
We clone the book content:
git clone https://github.com/lmweber/OSTA