olex2/README.md

@@ -1,25 +1,7 @@
-XDS
+# Olex2
 
-Step 1: login with your -adm account
+Olex2 is a free, open-source software program used for determining, visualizing, and analyzing small-molecule crystal structures. It provides a comprehensive and user-friendly graphical interface to guide users through the process of crystal structure solution, refinement, and report generation. This workflow-oriented program is designed to be useful for both experienced crystallographers and chemists who may not have specialized training.
 
-```
-[smith_k@ra-l-005 xds]$ kinit smith_k-adm
-[smith_k@ra-l-005 xds]$ aklog
-```
-
-Step 2: load the latest Pmodules package
-
-```
-module use unstable
-module load Pmodules/2.0.0
-```
-
-Step 3: go into olex2 directory, update config.yaml to add newest release version and build module with that release name (e.g. below is for 1.5)
-
-```
-cd olex2
-vi files/config.yaml
-./build 1.5
-```
-
-Step 4: confirm that the module loads as expected 
+## Installation guide
+1. First, download the zip archive with the binaries. For example for version 1.5, it was download from https://secure.olex2.org/olex2-distro/1.5/olex2-linux64.zip
+2. Build the module with the correct version.

olex2/build

@@ -1,15 +1,43 @@
 #!/usr/bin/env modbuild
 
+pbuild::configure(){
+    :
+}
 
-pbuild::prep() { :; }
-
-pbuild::configure() { :; }
-
-pbuild::compile() { :; }
+pbuild::compile(){
+    :
+}
 
 pbuild::install() {
-    #wget --no-check-certificate https://xds.mr.mpg.de/XDS-gfortran_Linux_x86_64.tar.gz
+
+    # Get the OS and architecture
+    os=$(uname -s | tr '[:upper:]' '[:lower:]')
+    arch=$(uname -m)
+    case "$arch" in
+        x86_64|amd64) arch="64" ;;
+        i386|i686)    arch="32" ;;
+        aarch64)      arch="arm64" ;;
+        armv7*)       arch="arm" ;;
+    esac
+
+    ZIP="${PREFIX}/${P}-${os}${arch}.zip"
+
+    # Copy the zip archive from the build directory
+    cp -n "${BUILDBLOCK_DIR}/${P}-${os}${arch}.zip" "$ZIP"
+
+    # Extract contents directly into PREFIX
+    unzip -o -q "$ZIP" -d "${PREFIX}"
+
+    # Create the bin directory
     mkdir -p "${PREFIX}/bin"
-    cd "${PREFIX}/bin"
-    unzip "${BUILDBLOCK_DIR}/Olex2Linux64.zip"
+
+    # Copy the executable files to the bin directory
+    find "${PREFIX}/${P}" -maxdepth 1 -type f -perm -111 -exec mv {} "${PREFIX}/bin/" \;
+    
+    # Move all contents of the zip archive into PREFIX
+    mv "${PREFIX}/${P}/"* "${PREFIX}/"
+    rmdir "${PREFIX}/${P}"
+
+    # Remove zip archive
+    rm "$ZIP"
 }

olex2/files/config.yaml

@@ -5,6 +5,7 @@ olex2:
     group: MX
     overlay: base
     relstage: stable
+
   versions:
     1.5:
       config:

olex2/modulefile

@@ -1,12 +1,18 @@
 #%Pmodule
 
-module-whatis       "OlexSys Ltd is a scientific software company providing State of the Art Crystallographic Software as well as the best Laboratory Chemicals Management there is."
-module-url          "https://www.olexsys.org/categories/installation/"
-module-license      "Olex2 is completely free to use for anyone. There is no catch here – whether you are in industry, academia or a student, it’s free!"
+module-whatis       "Olex2 is a free and comprehensive software package for determining, visualizing, and analyzing small-molecule crystal structures"
+module-url          "https://www.olexsys.org/olex2"
+module-license      "https://www.olexsys.org/tags/licence/"
 module-maintainer   "MX Data <jiaxin.duan@psi.ch>"
 
-module-help     "
-Olex2 is open source – all our code is available for you to look at, check and – hopefully!
+module-help         "
+Olex2 is a free and comprehensive software package for determining,
+visualizing, and analyzing small-molecule crystal structures. It features a
+user-friendly, mouse-driven graphical interface to assist both chemists and
+crystallographers with tasks like structure solution, refinement, and report
+generation. The program seamlessly links all aspects of the crystallography
+workflow into a single, intuitive package.
 "
 
-setenv          Olex2                     $PREFIX/bin
+# Use software OpenGL explicitly to avoid Vulkan drivers missing error
+setenv LIBGL_ALWAYS_SOFTWARE 1