Merge remote-tracking branch 'origin/build-xtrapol8'

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.

Xtrapol8/build

@@ -10,8 +10,12 @@ pbuild::compile() {
     :
 }
 pbuild::install(){
+    # modbuild does not fetch config.yaml urls, so download here;
+    # rm the tarball afterwards so it does not ship inside the module
     mkdir "$PREFIX/bin"
-    cd "$PREFIX/bin" 
-    tar -xf "${BUILDBLOCK_DIR}/Xtrapol8-${V_PKG}.tar.gz" --strip-components=1
+    cd "$PREFIX/bin"
+    wget -O "Xtrapol8-${V_PKG}.tar.gz" "https://github.com/ElkeDeZitter/Xtrapol8/archive/refs/tags/v.${V_PKG}.tar.gz"
+    tar -xf "Xtrapol8-${V_PKG}.tar.gz" --strip-components=1
+    rm "Xtrapol8-${V_PKG}.tar.gz"
 }
 

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]

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
+