Start here. The foundation.

Turns a bare Linux machine into one that can build scientific software - without needing administrator rights. One command and a few hours later the machine has its own self-contained toolbox, kept in a single folder, that neither touches nor depends on anything already installed on the machine.

One command builds a self-contained software foundation for the machine's architecture - ARM/aarch64 included - inside the extraction directory: a Gentoo Prefix, then EasyBuild + Lmod layered on top of it. Background build with the log tailed; every script refuses root. Lmod is emerged by the prefix's own portage and EasyBuild lives in a venv built from the prefix python, so nothing touches the host beyond reading its compiler.

activate.sh bin install.sh manifest prefix README.md run.R

• An unprivileged user - every script refuses UID 0
• gcc, g++, make, patch, tar, xz on the host image (preflight lists anything missing)
• Network for source fetches (portage tree, distfiles, PyPI)
• ~20 GB free and 2-6 h for the prefix stage; the EasyBuild layer is minutes
• A stable absolute path (e.g. /opt/prefix-install) - the tree is not relocatable

# from R, via the rxedn catalogue
rxedn::rxedn_install_module("prefix.extract.ndexr.io")

# the extraction lands at <domains_dir>/prefix.extract.ndexr.io/prefix-install/

No archive to unpack and no checksum to compare: rxedn publishes each repo as an immutable <host>-<sha7>.tar.gz and records its sha256 in the catalogue index, so the commit is the identity. Pull it, and the files are simply there.

# the extraction is a directory in this repo - copy it somewhere stable
cp -r prefix-install /opt/ && cd /opt/prefix-install   # see README on why the path must be stable

# from R (Workbench session) - session-core-aware kickoff:
#   source('run.R'); kickoff(); build_status(); tail_log()

./install.sh          # shell lane: prefix, then EasyBuild
bin/status.sh         # re-attach to the log any time

source activate.sh    # when done: eb + module on PATH
eb --rpath --robot GCC-13.3.0.eb

Output stays put, in prefix/<triple>/ and eb/ inside the extraction directory - nothing is copied out.

Generic prefix install (with EasyBuild)

Carried in manifest/ , verbatim - the declared set this extraction will build. It travels in the repo, so a copy taken to a machine with no route back here still knows the full list.