From 5f96777445812908b95427db093c81add9a00e03 Mon Sep 17 00:00:00 2001 From: duan_j Date: Tue, 28 Oct 2025 14:30:34 +0100 Subject: [PATCH 1/3] update DIALS to 3.25.0 but has unsupported integer dtype, reported to github page --- DIALS/.licence | 2 ++ DIALS/README.md | 25 +++++++++++++++++++++++++ DIALS/build | 20 ++++++++++++++++++++ DIALS/files/config.yaml | 11 +++++++++++ DIALS/modulefile | 14 ++++++++++++++ 5 files changed, 72 insertions(+) create mode 100644 DIALS/.licence create mode 100644 DIALS/README.md create mode 100644 DIALS/build create mode 100644 DIALS/files/config.yaml create mode 100644 DIALS/modulefile diff --git a/DIALS/.licence b/DIALS/.licence new file mode 100644 index 0000000..3d3b837 --- /dev/null +++ b/DIALS/.licence @@ -0,0 +1,2 @@ +# Paul Scherrer Institute, Macromolecular Crystallography + 3938465545 2992269931 2851646202 2685600639 2346109776 3745393523 diff --git a/DIALS/README.md b/DIALS/README.md new file mode 100644 index 0000000..72fd11f --- /dev/null +++ b/DIALS/README.md @@ -0,0 +1,25 @@ +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 diff --git a/DIALS/build b/DIALS/build new file mode 100644 index 0000000..4a4e3ad --- /dev/null +++ b/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 +} diff --git a/DIALS/files/config.yaml b/DIALS/files/config.yaml new file mode 100644 index 0000000..26c034a --- /dev/null +++ b/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 diff --git a/DIALS/modulefile b/DIALS/modulefile new file mode 100644 index 0000000..3cbe3fe --- /dev/null +++ b/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 " + +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 $PREFIX/dials-v3-25-0/dials_env.sh;" From 677f84307f35db727c4a841e5dffb1ef0389bf2f Mon Sep 17 00:00:00 2001 From: duan_j Date: Tue, 28 Oct 2025 15:22:47 +0100 Subject: [PATCH 2/3] resolved the unsupported dtype issue in DIALS following https://github.com/cctbx/dxtbx/pull/785/files by allowing /entry/data/data --- DIALS/README.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/DIALS/README.md b/DIALS/README.md index 72fd11f..20b2d1e 100644 --- a/DIALS/README.md +++ b/DIALS/README.md @@ -23,3 +23,8 @@ vi files/config.yaml ``` Step 4: confirm that the module loads as expected + +PS: +Unsupported dtype issue is resolved by changing modules/dxtbx/src/dxtbx/format/FormatNXmx.py +allowing the return of also /entry/data/data to the handle: +https://github.com/dials/dials/issues/3033 From 8df323db5e8b9c292981ed4e2ffda96b9c4f7fef Mon Sep 17 00:00:00 2001 From: duan_j Date: Wed, 19 Nov 2025 14:54:54 +0100 Subject: [PATCH 3/3] added olex2 for MX small molecules --- olex2/README.md | 25 +++++++++++++++++++++++++ olex2/build | 15 +++++++++++++++ olex2/files/config.yaml | 11 +++++++++++ olex2/modulefile | 12 ++++++++++++ 4 files changed, 63 insertions(+) create mode 100644 olex2/README.md create mode 100644 olex2/build create mode 100644 olex2/files/config.yaml create mode 100644 olex2/modulefile diff --git a/olex2/README.md b/olex2/README.md new file mode 100644 index 0000000..b36af2d --- /dev/null +++ b/olex2/README.md @@ -0,0 +1,25 @@ +XDS + +Step 1: login with your -adm account + +``` +[smith_k@ra-l-005 xds]$ 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 diff --git a/olex2/build b/olex2/build new file mode 100644 index 0000000..8553ea2 --- /dev/null +++ b/olex2/build @@ -0,0 +1,15 @@ +#!/usr/bin/env modbuild + + +pbuild::prep() { :; } + +pbuild::configure() { :; } + +pbuild::compile() { :; } + +pbuild::install() { + #wget --no-check-certificate https://xds.mr.mpg.de/XDS-gfortran_Linux_x86_64.tar.gz + mkdir -p "${PREFIX}/bin" + cd "${PREFIX}/bin" + unzip "${BUILDBLOCK_DIR}/Olex2Linux64.zip" +} diff --git a/olex2/files/config.yaml b/olex2/files/config.yaml new file mode 100644 index 0000000..834b761 --- /dev/null +++ b/olex2/files/config.yaml @@ -0,0 +1,11 @@ +--- +format: 1 +olex2: + defaults: + group: MX + overlay: base + relstage: stable + versions: + 1.5: + config: + relstage: stable diff --git a/olex2/modulefile b/olex2/modulefile new file mode 100644 index 0000000..54771e4 --- /dev/null +++ b/olex2/modulefile @@ -0,0 +1,12 @@ +#%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-maintainer "MX Data " + +module-help " +Olex2 is open source – all our code is available for you to look at, check and – hopefully! +" + +setenv Olex2 $PREFIX/bin