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io.github.pemsley.coot.yaml
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app-id: io.github.pemsley.coot
runtime: org.gnome.Platform
runtime-version: "47"
sdk: org.gnome.Sdk
command: coot
finish-args:
- --socket=x11
- --share=ipc
- --device=dri
- --filesystem=home
- --share=network
- --env=GDK_CORE_DEVICE_EVENTS=1
- --env=COOT_PREFIX=/app
- --env=GDK_DEBUG=gl-prefer-gl
cleanup:
- /include
- /lib/pkgconfig
- /lib/cmake
- /share/aclocal
- /share/doc
- /share/info
- /share/man
- "*.la"
- "*.a"
modules:
- deps/pypi-dependencies.json
- name: fftw2
buildsystem: autotools
config-opts:
- --enable-shared
- --enable-float
- --disable-static
sources:
- type: archive
url: https://fftw.org/fftw-2.1.5.tar.gz
sha256: f8057fae1c7df8b99116783ef3e94a6a44518d49c72e2e630c24b689c6022630
- type: shell
commands:
- cp /usr/share/gnu-config/config.sub .
- cp /usr/share/gnu-config/config.guess .
- name: mmdb2
buildsystem: autotools
config-opts:
- --enable-shared
- --disable-static
build-options:
cxxflags: "-g -O2"
sources:
- type: archive
url: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/mmdb2-2.0.22.tar.gz
sha256: a9646933ce9f34633e1ae4901f2383af0e5318d6490851328f5b6aa06195ab51
- name: libccp4
buildsystem: autotools
config-opts:
- --enable-shared
- --disable-static
- --disable-fortran
sources:
- type: archive
url: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/libccp4-6.5.1.tar.gz
sha256: 280b473d950cdf8837ef66147ec581104298b892399bd856f13b096f2395dbe5
- name: clipper4coot
buildsystem: autotools
config-opts:
- --enable-mmdb
- --enable-ccp4
- --enable-cif
- --enable-minimol
- --enable-cns
- --enable-shared
- --disable-static
build-options:
cxxflags: "-g -O2 -fno-strict-aliasing -Wno-narrowing"
sources:
- type: archive
url: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/clipper-2.1.20180802.tar.gz
sha256: 7c7774f224b59458e0faa104d209da906c129523fa737e81eb3b99ec772b81e0
- type: patch
path: clipper-configure-2.patch
- name: libgd
buildsystem: autotools
config-opts:
- --without-x
- --without-xpm
sources:
- type: archive
url: https://github.com/libgd/libgd/releases/download/gd-2.3.3/libgd-2.3.3.tar.xz
sha256: 3fe822ece20796060af63b7c60acb151e5844204d289da0ce08f8fdf131e5a61
- type: patch
path: gd.h.patch
- name: raster3d
buildsystem: simple
build-options:
cxxflags: "-g -O2 -fno-strict-aliasing -Wno-narrowing"
build-commands:
- make linux
- make all
- make install
sources:
- type: archive
url: http://www.bmsc.washington.edu/raster3d/Raster3D_3.0-7.tar.gz
sha256: f566b499fee341db3a95229672c6afdbdb69da7faabdbe34f6e0d332d766160c
- type: patch
path: Makefile.template.patch
- name: ssm
buildsystem: autotools
config-opts:
- --enable-ccp4
- --enable-shared
- --disable-static
build-options:
cflags: -fPIC
sources:
- type: archive
url: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/ssm-1.4.tar.gz
sha256: 56e7e64ed86d7d9ec59500fd34f26f881bdb9d541916d9a817c3bfb8cf0e9508
- name: boost
buildsystem: simple
build-commands:
- ./bootstrap.sh --without-icu --with-python=python3.12 --with-python-root=/usr --with-libraries=system,python,regex,thread,serialization,iostreams,program_options --prefix=/app --libdir=/app/lib
- ./b2 install --prefix=/app --libdir=/app/lib linkflags=-L/usr/lib python=3.12 -d2 -j$FLATPAK_BUILDER_N_JOBS threading=multi link=shared,static
build-options:
cflags: "-fPIC"
cxxflags: "-fPIC -std=c++14"
cleanup:
- /share/boost
sources:
- type: git
url: https://github.com/boostorg/boost.git
tag: boost-1.86.0
- name: libdwarf
buildsystem: autotools
config-opts:
- --enable-shared
sources:
- type: archive
url: https://www.prevanders.net/libdwarf-0.11.0.tar.xz
sha256: 846071fb220ac1952f9f15ebbac6c7831ef50d0369b772c07a8a8139a42e07d2
- name: gsl
buildsystem: autotools
sources:
- type: archive
url: https://ftp.gnu.org/gnu/gsl/gsl-2.8.tar.gz
sha256: 6a99eeed15632c6354895b1dd542ed5a855c0f15d9ad1326c6fe2b2c9e423190
- name: glm
buildsystem: cmake
config-opts:
- -DGLM_BUILD_TESTS=OFF
- -DBUILD_SHARED_LIBS=ON
sources:
- type: archive
url: https://github.com/g-truc/glm/archive/refs/tags/1.0.1.tar.gz
sha256: 9f3174561fd26904b23f0db5e560971cbf9b3cbda0b280f04d5c379d03bf234c
- name: openblas
buildsystem: cmake-ninja
builddir: true
config-opts:
- -DDYNAMIC_ARCH=1
- -DUSE_OPENMP=1
- -DNUM_THREADS=56
- -DNO_SVE=1
- -DBUILD_SHARED_LIBS=ON
- -DDYNAMIC_ARCH=ON
post-install:
- ln -s /app/lib/libopenblas.so /app/lib/libblas.so
- ln -s /app/lib/libopenblas.so /app/lib/liblapack.so
sources:
- type: archive
url: https://github.com/OpenMathLib/OpenBLAS/archive/refs/tags/v0.3.28.tar.gz
sha256: f1003466ad074e9b0c8d421a204121100b0751c96fc6fcf3d1456bd12f8a00a1
- name: bdw-gc
buildsystem: autotools
config-opts:
- --disable-debug
- --disable-docs
- --disable-dependency-tracking
sources:
- type: git
url: https://github.com/ivmai/bdwgc
tag: v8.2.4
- name: guile
buildsystem: autotools
config-opts:
- --with-libltdl-prefix=/app
- --with-libreadline-prefix=/app
sources:
- type: archive
url: https://ftp.gnu.org/gnu/guile/guile-2.2.7.tar.xz
sha256: cdf776ea5f29430b1258209630555beea6d2be5481f9da4d64986b077ff37504
- name: g-wrap
buildsystem: autotools
config-opts:
- --disable-Werror
sources:
- type: archive
url: http://savannah.nongnu.org/download/g-wrap/g-wrap-1.9.15.tar.gz
sha256: 0ff6e2700e74b457323726f7c2551a466d8ba44339705f6792d7b533145c602a
- name: guile-cairo
buildsystem: autotools
sources:
- type: archive
url: http://download.savannah.gnu.org/releases/guile-cairo/guile-cairo-1.10.0.tar.gz
sha256: ae3d7e0f0a8ae93d0a15c692514eb30f2478d407052064976fc59a291cccdd5c
- name: guile-lib
buildsystem: autotools
config-opts:
- --with-guile-site=yes
sources:
- type: archive
url: https://download.savannah.nongnu.org/releases/guile-lib/guile-lib-0.2.7.tar.gz
sha256: e4ef3b845f121882c7c0cf04f81a1cb8fd360c6f64b56b868de5546214f904de
- name: guile-gnome-platform
buildsystem: autotools
sources:
- type: archive
url: https://ftp.gnu.org/gnu/guile-gnome/guile-gnome-platform/guile-gnome-platform-2.16.5.tar.gz
sha256: 298d8c4f9b567bfe87beda18ed58d047c2e01b88c80895129de5466b921ccebe
- name: gemmi
buildsystem: cmake-ninja
sources:
- type: git
url: https://github.com/project-gemmi/gemmi.git
tag: v0.7.0
- name: swig
buildsystem: autotools
sources:
- type: git
url: https://github.com/swig/swig.git
tag: v4.3.0
- name: Catch2
buildsystem: cmake-ninja
builddir: true
config-opts:
- "-DCMAKE_CXX_STANDARD=17"
sources:
- type: archive
url: https://github.com/catchorg/Catch2/archive/refs/tags/v3.7.1.tar.gz
sha256: c991b247a1a0d7bb9c39aa35faf0fe9e19764213f28ffba3109388e62ee0269c
- name: eigen
buildsystem: cmake-ninja
builddir: true
sources:
- type: archive
url: https://gitlab.com/libeigen/eigen/-/archive/3.3.9/eigen-3.3.9.tar.gz
sha256: 7985975b787340124786f092b3a07d594b2e9cd53bbfe5f3d9b1daee7d55f56f
- name: rdkit
buildsystem: cmake-ninja
builddir: true
config-opts:
- -DCatch2_DIR=/app
- -DPYTHON_EXECUTABLE=/usr/bin/python3
- -DPYTHON_INCLUDE_DIR=/usr/include/python3.12
- -DRDK_BUILD_CAIRO_SUPPORT=ON
- -DRDK_INSTALL_INTREE=OFF
- -DRDK_INSTALL_COMIC_FONTS=OFF
- -DRDK_BUILD_MAEPARSER_SUPPORT=OFF
sources:
- type: git
url: https://github.com/rdkit/rdkit
tag: Release_2024_09_4
- type: archive
url: https://github.com/schrodinger/maeparser/archive/refs/tags/v1.3.1.tar.gz
sha256: a8d80f67d1b9be6e23b9651cb747f4a3200132e7d878a285119c86bf44568e36
strip-components: 0
- type: archive
url: https://github.com/schrodinger/coordgenlibs/archive/refs/tags/v3.0.2.tar.gz
sha256: f67697434f7fec03bca150a6d84ea0e8409f6ec49d5aab43badc5833098ff4e3
strip-components: 0
- type: archive
url: https://github.com/rareylab/RingDecomposerLib/archive/refs/tags/v1.1.3_rdkit.tar.gz
sha256: 944b5816712a48bbf88aa25d4300ce11871ddf6e971218eac08f90ed2192f715
strip-components: 0
- type: archive
url: https://github.com/ncbi/pubchem-align3d/archive/daefab3.tar.gz
sha256: 4871a08104c660890015f27d32a0147fc32df69a8962ca5cd1fe54ef6319c779
strip-components: 0
- type: archive
url: https://github.com/Tencent/rapidjson/archive/858451e.tar.gz
sha256: 765339356391422ad7f0258f8b746d8010da205762784a84980936e8b38e03ce
strip-components: 0
- type: shell
commands:
- mkdir -p External/CoordGen/{maeparser,coordgen}
- mkdir -p External/RingFamilies/RingDecomposerLib
- mkdir -p External/pubchem_shape/pubchem-align3d
- mkdir -p External/rapidjson-1.1.0
- cp -r maeparser-1.3.1/* External/CoordGen/maeparser
- cp -r coordgenlibs-3.0.2/* External/CoordGen/coordgen
- cp -r RingDecomposerLib-1.1.3_rdkit/* External/RingFamilies/RingDecomposerLib
- cp -r pubchem-align3d-daefab3dd0c90ca56da9d3d5e375fe4d651e6be3/* External/pubchem_shape/pubchem-align3d
- cp -r rapidjson-858451e5b7d1c56cf8f6d58f88cf958351837e53/* External/rapidjson-1.1.0
- name: coot
buildsystem: autotools
config-opts:
- --with-boost-libdir=/app/lib
- --with-rdkit-prefix=/app
- --with-guile
- --with-backward
- --with-libdw
build-options:
env:
GLM_CFLAGS: "-I/app/include"
GLM_LIBS: "-L/app/lib -lglm"
post-install:
- mv monomers-ccp4-9.0.000 monomers
- mkdir -p ${FLATPAK_DEST}/share/coot/lib/data && mv monomers ${FLATPAK_DEST}/share/coot/lib/data
- mv reference-structures ${FLATPAK_DEST}/share/coot
- cp -r python/ ${FLATPAK_DEST}/share/coot/
- install -Dm644 pixmaps/icons/coot.svg ${FLATPAK_DEST}/share/icons/hicolor/scalable/apps/${FLATPAK_ID}.svg
- install -Dm644 coot.desktop ${FLATPAK_DEST}/share/applications/${FLATPAK_ID}.desktop
- desktop-file-edit --set-key=Icon --set-value=${FLATPAK_ID} ${FLATPAK_DEST}/share/applications/${FLATPAK_ID}.desktop
- install -Dm644 coot.appdata.xml ${FLATPAK_DEST}/share/metainfo/${FLATPAK_ID}.metainfo.xml
sources:
- type: git
url: https://github.com/pemsley/coot.git
tag: Release-1.1.13
- type: patch
path: coot.appdata.xml.patch
- type: archive
url: https://github.com/MonomerLibrary/monomers/archive/refs/tags/ccp4-9.0.000.tar.gz
sha256: 7cc57fffb05202d7e8a407f91809a5b36ac23a1a3795656c662c7bdeaea28f57
strip-components: 0
- type: archive
url: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/reference-structures.tar.gz
sha256: 44db38506f0f90c097d4855ad81a82a36b49cd1e3ffe7d6ee4728b15109e281a
strip-components: 0