update BUSTER

BUSTER/README.md

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+# BUSTER
+
+BUSTER (Global Phasing Ltd.) — macromolecular refinement suite:
+`refine`, `grade2`, `rhofit`, `buster-report`, `pipedream`, ...
+Licence-gated: the PSI licence token is committed as `BUSTER/.licence`
+and installed into the software tree at build time.
+
+- Upstream: https://www.globalphasing.com/buster/
+- Install doc followed: https://www.globalphasing.com/buster/manual/installation/CentOS7_64bit/index.html
+
+## Dependencies (per the GPhL doc)
+
+| Doc requirement | On Ra |
+|---|---|
+| CCP4 (all components; also provides coot for `visualise-*-coot`) | `runtime_deps: ccp4/8.0` |
+| ImageMagick (buster-report) | `runtime_deps: ImageMagick/7.1.2-30` |
+| PyMOL (buster-report) | `runtime_deps: pymol-open-source/3.1.0` |
+| TeX/LaTeX (buster-report PDF) | system RPM — ask admins for `texlive` if missing |
+| CSD-Core (Grade2, Mogul validation) | not licensed on Ra → `BDG_CSD_TOP_DIRECTORY=none` |
+| autoPROC (optional, pipedream) | `module load autoPROC` by hand |
+
+The build writes `$PREFIX/setup_local.sh` (GPhL configure step) with
+`BDG_CSD_TOP_DIRECTORY=none` and the obsolete CSD variables unset, so
+Grade2 and Mogul checks are cleanly disabled. If PSI ever licenses
+CSD-Core, point that variable at the CCDC top dir (must contain
+`ccdc-software/`) and rebuild — or edit the installed file in place.
+The doc's `BUSTER_latest` symlink is not needed: Pmodules versioning
+covers it.
+
+## Build on Ra
+
+Stage the licence-gated snapshot by hand (download needs GPhL
+credentials, so no `urls:`): save it in this module dir as
+`BUSTER_snapshot_<date>.tar.gz` (gitignored). Then:
+
+```sh
+module use unstable && module load modbuild/2.1.3
+cd BUSTER
+modbuild build \
+    --tmpdir=/das/work/p21/p21515/.cache/Pmodules \
+    --distdir=/das/work/p21/p21515/.cache/Pmodules \
+    20240710
+module use MX unstable && module load BUSTER/20240710
+```
+
+## Verifying the install
+
+GPhL ships `checkdeps` exactly for this (~10 s; `-n` skips per-program
+prompts):
+
+```sh
+module load BUSTER/20240710
+checkdeps -n
+```
+
+Expected FINAL SUMMARY: SUCCESS for refine (licence), hydrogenate,
+buster-report, pipedream; grade/grade2 will FAIL by design (CSD
+disabled). `refine -h` should show licence info. Also run `checkdeps`
+once from a normal user account to catch permission issues.
+
+## Adding a new version
+
+Stage the new `BUSTER_snapshot_<date>.tar.gz` here, add the date under
+`versions:` in `files/config.yaml`, build as above. `setup_local.sh`
+carries over automatically (the build regenerates it).

BUSTER/build

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+#!/usr/bin/env modbuild
+
+pbuild::prep() { :; }
+
+pbuild::configure() { :; }
+
+pbuild::compile() { :; }
+
+pbuild::install() {
+    # BUSTER is licence-gated: the Global Phasing snapshot cannot be wget'd
+    # (download needs credentials), so stage it in this module dir first as
+    # BUSTER_snapshot_<snapshot-date>.tar.gz (gitignored), then unpack into $PREFIX.
+    # V_PKG (not V) so rebuilds as <date>-2, <date>-3 reuse the same staged tarball.
+    mkdir -p "${PREFIX}"
+    cd "${PREFIX}"
+    tar -xf "${BUILDBLOCK_DIR}/BUSTER_snapshot_${V_PKG}.tar.gz" --strip-components=1 || \
+        std::die 42 "BUSTER: untar failed - is BUSTER_snapshot_${V_PKG}.tar.gz staged in ${BUILDBLOCK_DIR}?"
+
+    # PSI licence token at the software home ($BDG_home) activates the suite
+    cp "${BUILDBLOCK_DIR}/.licence" "${PREFIX}/.licence" || \
+        std::die 42 "BUSTER: .licence token missing from module dir"
+
+    # GPhL configure step (doc section 6): no CSD-Core on Ra, so Grade2 and
+    # buster-report Mogul validation are disabled. Point BDG_CSD_TOP_DIRECTORY
+    # at a CCDC install top dir (contains ccdc-software/) if one ever arrives.
+    # The unset clears obsolete pre-May-2024 CSD variables per the doc.
+    cat > "${PREFIX}/setup_local.sh" <<'EOF'
+export BDG_CSD_TOP_DIRECTORY=none
+unset BDG_TOOL_MOGUL CSD_HOME BDG_TOOL_CSD_PYTHON_API
+EOF
+
+    [[ -r "${PREFIX}/setup.sh" ]] || \
+        std::die 42 "BUSTER: setup.sh missing at PREFIX root - check tarball layout / strip level"
+}

BUSTER/files/config.yaml

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+---
+format: 1
+BUSTER:
+  defaults:
+    group: MX
+    overlay: base
+    relstage: unstable
+  versions:
+    20240710:
+      config:
+        relstage: unstable
+        # Per GPhL install doc: CCP4 required by all components; ImageMagick +
+        # PyMOL required by buster-report. TeX/LaTeX (also buster-report) is a
+        # system RPM, no module. ImageMagick/pymol-open-source are still
+        # unstable - promote them before promoting BUSTER to stable.
+        runtime_deps: [ccp4/8.0, ImageMagick/7.1.2-30, pymol-open-source/3.1.0]

BUSTER/modulefile

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+#%Module1.0
+
+module-whatis       "BUSTER: macromolecular refinement suite (refine, grade2, rhofit, pipedream)"
+module-url          "https://www.globalphasing.com/buster/"
+module-license      "Global Phasing Ltd. proprietary licence"
+module-maintainer   "MX Data <jiaxin.duan@psi.ch>"
+
+module-help "
+BUSTER (Global Phasing Ltd.): refine, grade2, rhofit, buster-report,
+pipedream and friends. CCP4, ImageMagick and PyMOL come in as module
+dependencies; buster-report PDF output additionally needs system
+TeX/LaTeX. Grade2/Mogul validation is disabled (no CSD-Core licence
+on Ra) - use the Grade Web Server for non-confidential ligands.
+For pipedream's processing step, also: module load autoPROC
+"
+
+# BUSTER is activated by sourcing its setup script (sets BDG_home, PATH, etc.),
+# which in turn sources our setup_local.sh (CSD disabled).
+puts stdout "source $PREFIX/setup.sh;"