From 94cd0d8080b83a4197b13cd8e275815d8bd3942a Mon Sep 17 00:00:00 2001
From: Dawn <jiaxin.duan@psi.ch>
Date: Tue, 18 Aug 2026 15:29:16 +0200
Subject: [PATCH] Xtrapol8: add 1.2.9, ccp4 runtime dep, and missing modulefile
 env

XTRAPOL8_DIR and PATH were never set despite README referencing them;
upstream prerequisites require CCP4 alongside Phenix.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
---
 Xtrapol8/README.md         | 37 +++++++++++++++++++++++++++++++++++++
 Xtrapol8/files/config.yaml |  4 ++++
 Xtrapol8/modulefile        |  7 +++----
 3 files changed, 44 insertions(+), 4 deletions(-)

diff --git a/Xtrapol8/README.md b/Xtrapol8/README.md
index 11003d0..3ddc946 100644
--- a/Xtrapol8/README.md
+++ b/Xtrapol8/README.md
@@ -1,3 +1,40 @@
+# Xtrapol8
+
+Calculation of Fourier difference maps, extrapolated structure factor
+amplitudes (ESFAs) and occupancy estimation of low-occupancy triggered
+states. Built on cctbx; needs licensed Phenix (>=1.19) and CCP4 at runtime.
+
+- Upstream: https://github.com/ElkeDeZitter/Xtrapol8
+- License: MIT
+
+## How it is built
+
+Upstream installation is just "clone or download, keep all files in one
+directory". The recipe downloads the release tag tarball from GitHub and
+untars it into `$PREFIX/bin`. Loading the module sets `XTRAPOL8_DIR`,
+puts `$PREFIX/bin` on `PATH` and auto-loads phenix and ccp4.
+
+Note: release tags switched format at 1.2.8 (`v.1.2.8` with a dot);
+the default `urls:` matches the new style, so rebuilding <=1.2.5
+versions (tagged `v1.x.y`) would need a per-version `urls:` override.
+
+## Building on Ra
+
+```sh
+module use unstable && module load modbuild/2.1.2
+cd Xtrapol8
+modbuild build 1.2.9
+module use MX unstable && module load Xtrapol8/1.2.9
+```
+
+## Verifying the install
+
+```sh
+which Fextr.py                       # -> .../Xtrapol8/<version>/bin
+module list                          # phenix + ccp4 pulled in
+phenix.python "$XTRAPOL8_DIR/bin/Fextr.py"   # prints the argument list
+```
+
 ### Installation remarks
 
 March 2026: From v1.2.6 on, seem to work with phenix/1.21 versions. v1.2.8 is compiled with phenix/1.21 version and needs to be tested to see whether it works.
diff --git a/Xtrapol8/files/config.yaml b/Xtrapol8/files/config.yaml
index f153e36..b610f9c 100644
--- a/Xtrapol8/files/config.yaml
+++ b/Xtrapol8/files/config.yaml
@@ -13,3 +13,7 @@ Xtrapol8:
     1.2.8:
       config:
         runtime_deps: [phenix/1.21.1-5286]
+    1.2.9:
+      config:
+        # upstream prerequisites: Phenix >=1.19 AND CCP4 (both licensed)
+        runtime_deps: [phenix/1.21.1-5286, ccp4/8.0]
diff --git a/Xtrapol8/modulefile b/Xtrapol8/modulefile
index 6fc17b9..5bb7998 100644
--- a/Xtrapol8/modulefile
+++ b/Xtrapol8/modulefile
@@ -15,9 +15,8 @@ An introduction into Fourier difference maps, structure factor extrapolation and
 
 If Xtrapol8 was useful in your project, please cite us: De Zitter, E., Coquelle, N., Oeser, P., Barends, T. R. M., Colletier, J.-P., Xtrapol8 enables automatic elucidation of low-
 occupancy intermediate-states in crystallographic studies, Communications Biology, 5(1):640, 2022. (https://www.nature.com/articles/s42003-022-03575-7)
-
-    urls:
-      - url: https://github.com/ElkeDeZitter/Xtrapol8/archive/refs/tags/v${V_PKG}.tar.gz
-        name: Xtrapol8-${V_PKG}.tar.gz
 "
 
+setenv          XTRAPOL8_DIR    $PREFIX
+prepend-path    PATH            $PREFIX/bin
+