add adxv, imagemagick, and pymol-open-source

2026-09-01 10:43:13 +02:00
parent 1cf8491a57
commit 339626a467
12 changed files with 336 additions and 0 deletions
@@ -0,0 +1,48 @@
+# ImageMagick
+
+ImageMagick 7 image manipulation toolkit: `magick`, `convert`,
+`identify`, `mogrify`, `montage`, ... plus the MagickCore / MagickWand /
+Magick++ libraries.
+
+- Upstream: https://imagemagick.org/ (source: https://github.com/ImageMagick/ImageMagick)
+- License: ImageMagick License (Apache-2.0 derived)
+
+## How it is built
+
+Standard autotools from the sha-pinned GitHub tag tarball; the default
+modbuild hooks do `./configure --prefix=$PREFIX && make && make install`.
+Built with the gcc/12.3.0 module (also a runtime dep — Magick++ needs
+its libstdc++ on RHEL8). Version keys are the full upstream tag
+(`7.1.2-30`), which the download URL uses as `${V}`.
+
+Image-format delegates (PNG, JPEG, TIFF, ...) auto-enable from the
+`-devel` RPMs present on the build host. If a needed format is missing,
+install the RPM (e.g. `libpng-devel libjpeg-turbo-devel libtiff-devel`)
+and rebuild.
+
+## Building on Ra
+
+```sh
+module use unstable && module load modbuild/2.1.3
+cd ImageMagick
+modbuild build \
+    --tmpdir=/das/work/p21/p21515/.cache/Pmodules \
+    --distdir=/das/work/p21/p21515/.cache/Pmodules \
+    7.1.2-30
+module use MX unstable && module load ImageMagick/7.1.2-30
+```
+
+## Verifying the install
+
+```sh
+which magick                 # -> /opt/psi/MX/ImageMagick/7.1.2-30/bin/magick
+magick -version              # version + enabled features
+magick -list format | head   # delegates that got enabled
+magick rose: /tmp/rose.png   # end-to-end: writes a PNG (needs libpng delegate)
+```
+
+## Adding a new version
+
+Pick the tag from https://github.com/ImageMagick/ImageMagick/tags, add
+version + tarball sha256 in `files/config.yaml` (`sha256sum` the
+downloaded tag tarball), then build as above.
@@ -0,0 +1,11 @@
+#!/usr/bin/env modbuild
+
+# Plain autotools build: default hooks run ./configure --prefix=$PREFIX,
+# make -j, make install. Delegates (png/jpeg/tiff/...) auto-enable from
+# whatever -devel RPMs exist on the build host; `magick -list format`
+# shows what got in.
+
+pbuild::post_install() {
+    # modbuild has no errexit in hooks - without this a failed make still installs the modulefile
+    [[ -x "$PREFIX/bin/magick" ]] || std::die 42 "magick binary missing - configure/make failed above"
+}
@@ -0,0 +1,21 @@
+---
+format: 1
+ImageMagick:
+  defaults:
+    group: MX
+    overlay: base
+    relstage: unstable
+    urls:
+      # tag is the full version incl. patch release, e.g. 7.1.2-30 -> ${V}
+      - url: https://github.com/ImageMagick/ImageMagick/archive/refs/tags/${V}.tar.gz
+        name: ImageMagick-${V}.tar.gz
+        strip_dirs: 1
+  shasums:
+    ImageMagick-7.1.2-30.tar.gz: 3034a64f22398e15ee3dd1e6b1aa83d838cfc47df1bb246ae0eca9590e6ace72
+  versions:
+    7.1.2-30:
+      config:
+        relstage: unstable
+        # gcc also at runtime: Magick++ links gcc-12 libstdc++, newer than RHEL8 system one
+        build_requires: [gcc/12.3.0]
+        runtime_deps: [gcc/12.3.0]
@@ -0,0 +1,18 @@
+#%Module1.0
+
+module-whatis       "ImageMagick - create, edit and convert bitmap images (magick, convert, ...)"
+module-url          "https://imagemagick.org/"
+module-license      "ImageMagick License (Apache-2.0 derived)"
+module-maintainer   "MX Data <jiaxin.duan@psi.ch>"
+
+module-help     "
+ImageMagick 7 command-line tools (magick, convert, mogrify, identify,
+montage, ...) plus MagickCore/MagickWand/Magick++ libraries and
+pkg-config files. Enabled image formats depend on the -devel RPMs
+present at build time: check with `magick -list format`.
+"
+
+prepend-path    PATH               $PREFIX/bin
+prepend-path    LD_LIBRARY_PATH    $PREFIX/lib
+prepend-path    PKG_CONFIG_PATH    $PREFIX/lib/pkgconfig
+prepend-path    MANPATH            $PREFIX/share/man
@@ -0,0 +1,41 @@
+# adxv
+
+Adxv — display and analyze X-ray diffraction images (ADSC, MarCCD, CBF,
+XDS `.pck`, EDF, NumPy, HDF5, TIFF, raw ...). X11/Motif GUI.
+
+- Upstream: https://adxv.scripps.edu/ (manual: https://adxv.scripps.edu/adxv/AdxvUserManual.pdf)
+- License: free for everyone, no registration/fee; binary-only, no source
+
+## How it is built
+
+No build: the recipe downloads the prebuilt, sha-pinned
+`adxv.x86_64CentOS7` binary (CentOS7 build runs fine on RHEL8) and
+installs it as `$PREFIX/bin/adxv`. Runtime needs system X11 + Motif
+(`motif` RPM, libXm) on the execution host and an X server.
+
+## Building on Ra
+
+```sh
+module use unstable && module load modbuild/2.1.3
+cd adxv
+modbuild build \
+    --tmpdir=/das/work/p21/p21515/.cache/Pmodules \
+    --distdir=/das/work/p21/p21515/.cache/Pmodules \
+    1.9.15
+module use MX unstable && module load adxv/1.9.15
+```
+
+## Verifying the install
+
+```sh
+which adxv          # -> /opt/psi/MX/adxv/1.9.15/bin/adxv
+ldd $(which adxv)   # no "not found" lines (libXm etc. resolve)
+adxv -help          # usage text; GUI itself needs X
+```
+
+## Adding a new version
+
+Check the download section on https://adxv.scripps.edu/adxv.html for the
+new `adxv_<ver>/adxv.x86_64CentOS7` path, add version + binary sha256 in
+`files/config.yaml` (`sha256sum` the downloaded binary), then build as
+above.
@@ -0,0 +1,19 @@
+#!/usr/bin/env modbuild
+
+# Prebuilt single binary from adxv.scripps.edu (CentOS7 build, runs on RHEL8;
+# needs system Motif/X11 libs at runtime). Default pbuild::prep downloads +
+# sha-verifies + copies it into SRC_DIR (unpacker: none).
+
+pbuild::configure() {
+    :
+}
+
+pbuild::compile() {
+    :
+}
+
+pbuild::install() {
+    mkdir -p "$PREFIX/bin"
+    install -m 755 "$SRC_DIR/adxv-${V_PKG}.x86_64CentOS7" "$PREFIX/bin/adxv" || \
+        std::die 42 "adxv binary missing from SRC_DIR - download failed?"
+}
@@ -0,0 +1,19 @@
+---
+format: 1
+adxv:
+  defaults:
+    group: MX
+    overlay: base
+    relstage: unstable
+    urls:
+      # single prebuilt binary, no unpack; version-tagged name so the
+      # distfiles cache keeps one per release
+      - url: https://adxv.scripps.edu/adxv/adxv_${V_PKG}/adxv.x86_64CentOS7
+        name: adxv-${V_PKG}.x86_64CentOS7
+        unpacker: none
+  shasums:
+    adxv-1.9.15.x86_64CentOS7: 4df30c2ddb579ae3aa9d99895c74fd6ab332c3a290fb32bb9e8271a5d578e461
+  versions:
+    1.9.15:
+      config:
+        relstage: unstable
@@ -0,0 +1,15 @@
+#%Module1.0
+
+module-whatis       "Adxv - display and analyze X-ray diffraction images"
+module-url          "https://adxv.scripps.edu/"
+module-license      "Free for everyone, no registration or fee (binary-only)"
+module-maintainer   "MX Data <jiaxin.duan@psi.ch>"
+
+module-help     "
+Adxv displays 2-D area detector data (ADSC, MarCCD, CBF, XDS .pck,
+EDF, NumPy, HDF5, TIFF, raw, ...) as cross section, image or 3-D
+surface. X11/Motif app: needs an X server, and system Motif libs
+on the execution host.
+"
+
+prepend-path    PATH    $PREFIX/bin
@@ -0,0 +1,57 @@
+# pymol-open-source
+
+Open-Source PyMOL, compiled from the GitHub source. Free for everyone,
+no license file — unlike the `pymol` module (Schrodinger incentive
+bundle).
+
+- Upstream: https://github.com/schrodinger/pymol-open-source
+- License: Open-Source PyMOL license (BSD-like)
+
+## How it is built
+
+uv route (careless-style): uv fetches a standalone Python 3.12 into
+`$PREFIX/python`, creates `$PREFIX/venv`, then `uv pip install` compiles
+the sha-pinned source tarball into it with the gcc/12.3.0 module
+(`CC=gcc CXX=g++`; gcc is also a runtime dep for its libstdc++). glm
+(header-only) is fetched as a second pinned tarball and staged via
+`PREFIX_PATH`. PyQt5 is pip-installed for the GUI.
+
+Build options passed as `uv pip install -C k=v` (upstream
+`_custom_build/backend.py` turns them into `build_ext --k=v`):
+
+- `use-msgpackc=no` — no msgpack-c/mmtf-cpp on Ra; disables fast MMTF load
+- `no-libxml=yes` — disables COLLADA export
+- `no-vmd-plugins=no` — disables VMD molfile plugins (needs libnetcdf).
+  `no` is correct: upstream stores the value straight into `vmd_plugins`.
+
+Required system RPMs on the build host (if the compile fails, ask
+sysadmins for): `glew-devel libpng-devel freetype-devel mesa-libGL-devel`.
+
+`uv` must be on the build host (default `~/.local/bin/uv`, override with
+`UV=/path/to/uv`).
+
+## Building on Ra
+
+```sh
+module use unstable && module load modbuild/2.1.3
+cd pymol-open-source
+modbuild build \
+    --tmpdir=/das/work/p21/p21515/.cache/Pmodules \
+    --distdir=/das/work/p21/p21515/.cache/Pmodules \
+    3.1.0
+module use MX unstable && module load pymol-open-source/3.1.0
+```
+
+## Verifying the install
+
+```sh
+which pymol                              # -> .../pymol-open-source/3.1.0/venv/bin/pymol
+readlink -f "$PYMOL_ENV/bin/python"      # must resolve inside the module PREFIX
+pymol -cq                                # headless no-op: exits 0 without X
+pymol                                    # Qt GUI check, needs X
+```
+
+## Adding a new version
+
+Add the version + tarball sha256 in `files/config.yaml`
+(`sha256sum` the downloaded `v<ver>.tar.gz`), then build as above.
@@ -0,0 +1,45 @@
+#!/usr/bin/env modbuild
+
+# Open-source PyMOL, compiled from the GitHub source tarball into a uv venv
+# (careless-style uv route; conda unreachable from Ra). Default pbuild::prep
+# downloads + sha-verifies + unpacks both urls from files/config.yaml.
+# GLEW/libpng/freetype/GL headers must exist as system RPMs on the build host;
+# msgpack/MMTF, libxml2 (COLLADA) and VMD plugins (libnetcdf) are disabled
+# because those libs are not on Ra.
+
+pbuild::configure() {
+    # modbuild's shell strips ~/.local/bin from PATH; override with UV=/path/to/uv if needed
+    UV="${UV:-$HOME/.local/bin/uv}"
+    # ~/.cache/uv hits the home disk quota; shared cache reuses wheels across MX builds
+    export UV_CACHE_DIR="/opt/psi/MX/.uv-cache"
+    # keep the standalone CPython inside PREFIX so venv symlinks never point at a home cache
+    export UV_PYTHON_INSTALL_DIR="$PREFIX/python"
+    "$UV" venv --python 3.12 "$PREFIX/venv" || std::die 42 "uv venv failed - is uv at \$UV?"
+
+    # stage glm where setup.py's PREFIX_PATH lookup expects it: <prefix>/include/glm
+    mkdir -p "$SRC_DIR/deps/include"
+    cp -r "$SRC_DIR/glm-1.0.1/glm" "$SRC_DIR/deps/include/" || \
+        std::die 42 "glm staging failed - glm tarball missing from SRC_DIR?"
+}
+
+pbuild::compile() {
+    :
+}
+
+pbuild::install() {
+    UV="${UV:-$HOME/.local/bin/uv}"
+    export UV_CACHE_DIR="/opt/psi/MX/.uv-cache"
+    # force the gcc module's compilers; uv's standalone CPython records clang in sysconfig
+    export CC=gcc CXX=g++
+    export PREFIX_PATH="$SRC_DIR/deps"
+    # -C k=v reaches setup.py as `build_ext --k=v` (_custom_build/backend.py).
+    # no-vmd-plugins=no is deliberate: upstream dest is vmd_plugins, so `no` disables them.
+    "$UV" pip install --python "$PREFIX/venv/bin/python" \
+        -C use-msgpackc=no -C no-libxml=yes -C no-vmd-plugins=no \
+        "$SRC_DIR" || \
+        std::die 42 "pymol build failed - check system devel RPMs (glew, libpng, freetype, mesa-libGL)"
+    # Qt GUI; without it pymol falls back to CLI-only
+    "$UV" pip install --python "$PREFIX/venv/bin/python" PyQt5 || \
+        std::die 42 "PyQt5 install failed"
+    [[ -x "$PREFIX/venv/bin/pymol" ]] || std::die 42 "pymol launcher missing from venv"
+}
@@ -0,0 +1,26 @@
+---
+format: 1
+pymol-open-source:
+  defaults:
+    group: MX
+    overlay: base
+    relstage: unstable
+    urls:
+      - url: https://github.com/schrodinger/pymol-open-source/archive/refs/tags/v${V_PKG}.tar.gz
+        name: pymol-open-source-${V_PKG}.tar.gz
+        strip_dirs: 1
+      # glm is header-only and not packaged on Ra; staged into PREFIX_PATH by
+      # pbuild::configure. Pinned, version-independent of pymol.
+      - url: https://github.com/g-truc/glm/archive/refs/tags/1.0.1.tar.gz
+        name: glm-1.0.1.tar.gz
+  shasums:
+    pymol-open-source-3.1.0.tar.gz: 54306d65060bd58ed8b3dab1a8af521aeb4fd417871f15f463ff05ccb4e121fe
+    glm-1.0.1.tar.gz: 9f3174561fd26904b23f0db5e560971cbf9b3cbda0b280f04d5c379d03bf234c
+  versions:
+    3.1.0:
+      config:
+        relstage: unstable
+        # gcc also at runtime: the compiled _cmd extension needs gcc-12 libstdc++,
+        # newer than the RHEL8 system one
+        build_requires: [gcc/12.3.0]
+        runtime_deps: [gcc/12.3.0]
@@ -0,0 +1,16 @@
+#%Module1.0
+
+module-whatis       "PyMOL (open-source build) - molecular visualization system"
+module-url          "https://github.com/schrodinger/pymol-open-source"
+module-license      "Open-Source PyMOL license (BSD-like), free for everyone"
+module-maintainer   "MX Data <jiaxin.duan@psi.ch>"
+
+module-help     "
+Open-Source PyMOL, compiled from source into a private Python venv
+with the PyQt5 GUI. No license file needed (unlike the pymol
+incentive module). MMTF fast load, COLLADA export and VMD plugins
+are disabled in this build.
+"
+
+setenv          PYMOL_ENV   $PREFIX/venv
+prepend-path    PATH        $PREFIX/venv/bin