Merge branch 'main' into olex2_1.5

Reviewed-on: #16

DIALS/.licence

@@ -0,0 +1,2 @@
+# Paul Scherrer Institute, Macromolecular Crystallography
+ 3938465545 2992269931 2851646202 2685600639 2346109776 3745393523

DIALS/README.md

@@ -0,0 +1,30 @@
+XDS
+
+Step 1: login with your -adm account
+
+```
+kinit xxxx_x-adm
+aklog
+```
+
+Step 2: load the latest Pmodules package
+
+```
+module use unstable
+module load Pmodules/2.0.0
+```
+
+Step 3: go into DIALS directory, update config.yaml to add newest release version and build module with that release name
+
+```
+cd DIALS
+vi files/config.yaml
+./build 3.25.0
+```
+
+Step 4: confirm that the module loads as expected 
+
+PS:
+Unsupported dtype issue is resolved by changing modules/dxtbx/src/dxtbx/format/FormatNXmx.py
+allowing the return of also /entry/data/data to the handle:
+https://github.com/dials/dials/issues/3033

DIALS/build

@@ -0,0 +1,20 @@
+#!/usr/bin/env modbuild
+
+
+pbuild::prep() { :; }
+
+pbuild::configure() { :; }
+
+pbuild::compile() { :; }
+
+pbuild::install() {
+    cd "${PREFIX}"
+    wget https://dials.diamond.ac.uk/diamond_builds/dials-linux-x86_64-conda3.tar.xz
+    tar -xJf dials-linux-x86_64-conda3.tar.xz
+    cd dials-installer-dev
+    ./install --prefix=$PREFIX
+    cd "${PREFIX}"
+    rm dials-linux-x86_64-conda3.tar.xz
+    rm -r dials-installer-dev
+    ln -s dials-dev20251026 dials-v3-25-0
+}

DIALS/files/config.yaml

@@ -0,0 +1,11 @@
+---
+format: 1
+DIALS:
+  defaults:
+    group: MX
+    overlay: base
+    relstage: stable
+  versions:
+    3.25.0:
+      config:
+        relstage: unstable

DIALS/modulefile

@@ -0,0 +1,14 @@
+#%Module1.0
+
+module-whatis	        "DIALS: Diffraction Integration for Advanced Light Sources"
+module-url		"https://dials.github.io/"
+module-license	        "DIALS license"
+module-maintainer       "Jiaxin Duan <jiaxin.duan@psi.ch>"
+
+module-help	"
+X-ray crystallography for structural biology has benefited greatly from a number of advances in recent years including high performance pixel array detectors, new beamlines capable of delivering micron and sub-micron focus and new light sources such as X-FELs. The DIALS project is a collaborative endeavour to develop new diffraction integration software to meet the data analysis requirements presented by these recent advances. There are three end goals: to develop an extensible framework for the development of algorithms to analyse X-ray diffraction data; the implementation of algorithms within this framework and finally a set of user facing tools using these algorithms to allow integration of data from diffraction experiments on synchrotron and free electron sources.
+
+License : https://dials.github.io/license.html
+"
+
+puts stdout "source $PREFIX/dials-v3-25-0/dials_env.sh;"

Rosetta/README.md

@@ -1,18 +1,5 @@
-### Rosetta installation remarks: 
+# Rosetta
 
-As of July 2024, phenix 1.21 exists, and also Rosetta 3.14. These do not work together , as phenix/1.21.1 misses a file called command_line.py , which is existent in phenix 1.20  and is required for Rosetta. Also the compilation of phenix+Rosetta fails on RH7, so def needs to be done on RH8 nodes (Ra) and Rosetta 3.14 fails during compilation.  --> check  for new phenix releases if the compatabilty with Rosetta latest release was tested etc .
- 
-As a result, phenix/1.20 plus Rosetta 3.13 is used. (July 2024)
- 
-The installation of Rosetta +phenix requires a fully functional new phenix installation. A phenix command is run after the installation of Rosetta that builds the interface between the two:
- - Install phenix ( see phenix ) 
- - Install Rosetta as usual (see Pmodules MX Rosetta build script)
- - copy the site.settings file into the correct folder as described in "NOTE: On linux, if you are using GCC 5.1 or later (Ubuntu 16.04 or later), there is an ABI change that requires an additional flag to allow linking between our CentOS 6 binary build and Rosetta. To apply this flag, copy this site.settings file to ${PHENIX_ROSETTA_PATH}/main/source/tools/build/site.settings before running this final step" "(https://phenix-online.org/documentation/reference/rosetta_install.html)
- - then run the command
- 
- rosetta.build_phenix_interface nproc=10
- 
- - run rosetta.run_tests to test it.
- 
- IMPORTANT, both phenix and rosetta need to have the same file permisssions /owner as described in the phenix readme. In both cases the recommendation is to do it as -adm account on /afs/psi.ch/group/HPCE/user/xxx  and then run the installation from there (RH8 needed, RA therefore )
+The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures. It has enabled notable scientific advances in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes.
 
+https://github.com/RosettaCommons/rosetta

Rosetta/build

@@ -1,21 +1,21 @@
 #!/usr/bin/env modbuild
 
-pbuild::prep(){
-    :
-}
-
-pbuild::configure(){
+pbuild::configure() {
     :
 }
 
 pbuild::compile() {
-    :
+    cd "$SRC_DIR/main/source" || exit 1
+    ./scons.py -j10 mode=release bin
 }
 
 pbuild::install() {
-    mkdir "$PREFIX"
-    cd "$PREFIX"
-    tar -xf "${PMODULES_DISTFILESDIR}/Rosetta-${V}.tgz" --strip-components=1
+    # Copy the contents of the source code into <PREFIX>
+    cp -r "$SRC_DIR/main/"* "$PREFIX/"
+
+    # Ensure target directory exists
+    mkdir -p "$PREFIX/bin"
+
+    # Copy compiled binaries to the installation directory
+    install -m 755 "$SRC_DIR/main/source/bin/"* "$PREFIX/bin/"
 }
-
-

Rosetta/files/config.yaml

@@ -1,3 +1,5 @@
+---
+# yamllint disable rule:line-length
 format: 1
 Rosetta:
   defaults:
@@ -5,7 +7,32 @@ Rosetta:
     overlay: base
     relstage: unstable
     urls:
-      - url: https://www.rosettacommons.org/downloads/academic/3.13/rosetta_bin_linux_3.13_bundle.tgz
-        name: Rosetta-${V}.tgz
+      - url: https://downloads.rosettacommons.org/downloads/academic/${V_PKG}/rosetta_source_${V_PKG}_bundle.tar.bz2
+
+  shasums:
+    rosetta_source_3.15_bundle.tar.bz2: ac4665fb0173ac1e1ed060d4a894964d14a32aba49e3ee2f3f50e83c26ba0fb1
+
   versions:
-    3.13:
+    3.15:
+      variants:
+        - overlay: base 
+          systems: [.*.merlin7.psi.ch]
+          target_cpus: [x86_64]
+          relstage: unstable
+          build_requires:
+            - gcc/12.3.0
+            - Python/3.9.21
+          runtime_deps:
+            - gcc/12.3.0
+            - Python/3.9.21
+        - overlay: base 
+          target_cpus: [aarch64]
+          systems: [gpu0.*.merlin7.psi.ch]
+          relstage: unstable
+          build_requires:
+            - gcc/12.3.0
+            - Python/3.9.21
+          runtime_deps:
+            - gcc/12.3.0
+            - Python/3.9.21
+

Rosetta/modulefile

@@ -1,25 +1,14 @@
 #%Module1.0
 
-module-whatis	        "Rosetta™ is a molecular modeling software package for understanding protein structures, protein design, protein docking, protein-DNA and protein-protein interactions."
-module-url		         "https://www.rosettacommons.org/home"
-module-license	        "Academic License"
-module-maintainer       "greta.assmann@psi.ch>"
+module-whatis       "The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures"
+module-url          "https://github.com/RosettaCommons/rosetta"
+module-license      "Rosetta Software Non-Commercial License Agreement (https://github.com/RosettaCommons/rosetta?tab=License-1-ov-file)"
+module-maintainer   "João Pedro Agostinho de Sousa <joao.agostinho-de-sousa@psi.ch>"
 
-module-help	"
-The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures. It has enabled notable scientific advances in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes
-.
-
-Rosetta development began in the laboratory of Dr. David Baker at the University of Washington as a structure prediction tool but since then has been adapted to solve common computational macromolecular problems.
-
-Development of Rosetta has moved beyond the University of Washington into the members of RosettaCommons, which include government laboratories, institutes, research centers, and partner corporations.
-
-The Rosetta community has many goals for the software, such as:
-
-    Understanding macromolecular interactions
-    Designing custom molecules
-    Developing efficient ways to search conformation and sequence space
-    Finding a broadly useful energy functions for various biomolecular representations
+module-help         "
+The Rosetta software suite includes algorithms for computational modeling and
+analysis of protein structures. It has enabled notable scientific advances in
+computational biology, including de novo protein design, enzyme design, ligand
+docking, and structure prediction of biological macromolecules and
+macromolecular complexes.
 "
-
-prepend-path   PHENIX_ROSETTA_PATH     $PREFIX
-

autoPROC/.licence

@@ -1,2 +1,2 @@
 # Paul Scherrer Institute, Macromolecular Crystallography
- 3938465545 2992269931 1270736646   89765919 2346109776 3745393523
+ 3938465545 2992269931 2851646202 2685600639 2346109776 3745393523

olex2/README.md

@@ -0,0 +1,7 @@
+# Olex2
+
+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.
+
+## 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

@@ -0,0 +1,43 @@
+#!/usr/bin/env modbuild
+
+pbuild::configure(){
+    :
+}
+
+pbuild::compile(){
+    :
+}
+
+pbuild::install() {
+
+    # 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 "${PREFIX}/bin"
+
+    # Copy the executable files to the bin directory
+    find "${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

@@ -0,0 +1,12 @@
+---
+format: 1
+olex2:
+  defaults:
+    group: MX
+    overlay: base
+    relstage: stable
+
+  versions:
+    1.5:
+      config:
+        relstage: stable

olex2/modulefile

@@ -0,0 +1,18 @@
+#%Pmodule
+
+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 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.
+"
+
+# Use software OpenGL explicitly to avoid Vulkan drivers missing error
+setenv LIBGL_ALWAYS_SOFTWARE 1

xds/build

@@ -8,8 +8,8 @@ pbuild::configure() { :; }
 pbuild::compile() { :; }
 
 pbuild::install() {
-    wget --no-check-certificate https://xds.mr.mpg.de/XDS-INTEL64_Linux_x86_64.tar.gz
+    #wget --no-check-certificate https://xds.mr.mpg.de/XDS-gfortran_Linux_x86_64.tar.gz
     mkdir -p "${PREFIX}/bin"
     cd "${PREFIX}/bin"
-    tar -xf "${BUILDBLOCK_DIR}/XDS-INTEL64_Linux_x86_64.tar.gz" --strip-components=1
-}
+    tar -xf "${BUILDBLOCK_DIR}/XDS-gfortran_Linux_x86_64.tar.gz" --strip-components=1
+}

xds/files/config.yaml

@@ -6,4 +6,6 @@ xds:
     overlay: base
     relstage: stable
   versions:
-    20240724:
+    20250523:
+      config:
+        relstage: stable

xds/modulefile

@@ -3,10 +3,10 @@
 module-whatis       "X-ray Detector Software for processing single-crystal monochromatic diffraction data recorded by the rotation method"
 module-url          "http://xds.mpimf-heidelberg.mpg.de/"
 module-license      "XDS is free of charge for non-commercial applications"
-module-maintainer   "MX Data <mx-software@psi.ch>"
+module-maintainer   "MX Data <jiaxin.duan@psi.ch>"
 
 module-help     "
 XDS can process data images from CCD-, imaging-plate-, multiwire-, and pixel-detectors in a variety of formats as well as from multi-segment detectors assembled from several rectangular components in arbitrary arrangement.
 "
 
-setenv          XDS                     $PREFIX/bin
+setenv          XDS                     $PREFIX/bin