From f6b63e740d7a8e2d362187d8f78c5295420f1806 Mon Sep 17 00:00:00 2001
From: Duan <jiaxin.duan@psi.ch>
Date: Fri, 16 Oct 2026 17:49:09 +0200
Subject: [PATCH] olex2: export OLEX2_ROOT from the modulefile, use it in the
 README checks

---
 olex2/README.md  | 19 ++++++++++---------
 olex2/modulefile |  7 ++++++-
 2 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/olex2/README.md b/olex2/README.md
index 7eb20f6..52bcfc3 100644
--- a/olex2/README.md
+++ b/olex2/README.md
@@ -57,7 +57,9 @@ exports `OLEX2_CCTBX_DIR`, `BOOST_ADAPTBX_*`, `OLEX2_GL_*`,
 inherited one would be imported by the embedded Python 3.8 and break it),
 sets `LIBGL_ALWAYS_SOFTWARE=1` for the GUI only, then `exec`s the binary.
 `unirun` is never run: `/opt/psi/MX` is shared and read-only, updates are
-done by building a new module version.
+done by building a new module version. The modulefile exports
+`OLEX2_ROOT=$PREFIX` (our own name; the vendor's `OLEX2_DIR` re-targets the
+updater and stays unset) and puts `$PREFIX/bin` on `PATH`.
 
 ### Bundled glibc 2.39 sysroot (why and how)
 
@@ -147,12 +149,11 @@ GTK2/X11/OpenGL — also `olex2c` (wx is linked in statically). Check once
 per host type:
 
 ```sh
-module load olex2/1.5-7665
-P=/opt/psi/MX/olex2/1.5-7665
-$P/sysroot/usr/lib64/ld-linux-x86-64.so.2 --list $P/olex2c | grep -E 'not found|libc.so.6|libstdc'
+module load olex2/1.5-7665          # exports OLEX2_ROOT=/opt/psi/MX/olex2/1.5-7665
+$OLEX2_ROOT/sysroot/usr/lib64/ld-linux-x86-64.so.2 --list $OLEX2_ROOT/olex2c | grep -E 'not found|libc.so.6|libstdc'
 ```
 
-`libc.so.6`/`libstdc++.so.6` must resolve under `$P/sysroot`; every `not
+`libc.so.6`/`libstdc++.so.6` must resolve under `$OLEX2_ROOT/sysroot`; every `not
 found` line is a host package to `dnf install` (expected candidates on a
 minimal RHEL9: `gtk2`, `mesa-libGL`, `mesa-libGLU`, `libSM`, `libXxf86vm`,
 `libxkbcommon`). Plain `ldd` on the raw binary also works after the patch
@@ -161,13 +162,13 @@ minimal RHEL9: `gtk2`, `mesa-libGL`, `mesa-libGLU`, `libSM`, `libXxf86vm`,
 ## Verifying the install
 
 ```sh
-which olex2c            # -> /opt/psi/MX/olex2/1.5-7665/bin/olex2c
-which olex2             # -> /opt/psi/MX/olex2/1.5-7665/bin/olex2
-cat /opt/psi/MX/olex2/1.5-7665/version.txt   # SVN Revision No. 7665
+which olex2c            # -> $OLEX2_ROOT/bin/olex2c  (= /opt/psi/MX/olex2/1.5-7665/bin/olex2c)
+which olex2             # -> $OLEX2_ROOT/bin/olex2
+cat $OLEX2_ROOT/version.txt   # SVN Revision No. 7665
 
 # console: starts, loads a shipped sample, refines, exits (writes to ~/.olex2
 # and to a scratch copy of the sample - run it in a scratch dir)
-cd $(mktemp -d) && cp /opt/psi/MX/olex2/1.5-7665/sample_data/sucrose/* .
+cd $(mktemp -d) && cp $OLEX2_ROOT/sample_data/sucrose/* .
 olex2c                  # interactive prompt; then type:
 #   reap sucrose.res
 #   refine 4
diff --git a/olex2/modulefile b/olex2/modulefile
index fbf9680..492fb9a 100644
--- a/olex2/modulefile
+++ b/olex2/modulefile
@@ -22,6 +22,11 @@ Per-user data (DataDir) lives in ~/.olex2. The vendor Python API (olx, olex
 modules) is only available from inside olex2/olex2c, not as a system python.
 "
 
+# Install root (= Olex2 BaseDir): sample_data, sysroot, version.txt live here.
+# Our own name on purpose - OLEX2_DIR is a vendor variable that re-targets
+# the auto-updater, so it must stay unset.
+setenv          OLEX2_ROOT  $PREFIX
+
 # Launchers only: the raw binaries, the vendor 'start' script (auto-updater)
 # and the private python live under $PREFIX root and stay off PATH.
-prepend-path    PATH    $PREFIX/bin
+prepend-path    PATH        $PREFIX/bin