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Merge pull request #321 from mariux64/add-pymol-open-source-3.1.0-0
pymol-open-source: update to 3.1.0
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| #! /bin/bash | ||
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| # COOKIE=$(mcookie|cut -c-8); grep -v V_GREP_ME $0 > /dev/shm/runme-$COOKIE.sh ; sleep 0.3; exec bash /dev/shm/runme-$COOKIE.sh | ||
| # TESTING=1 | ||
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| PKG=pymol-open-source | ||
| VERSION=3.1.0 | ||
| BUILD=0 | ||
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| PREFIX=/pkg/$PKG-$VERSION-$BUILD | ||
| if [ -n "$TESTING" ]; then PREFIX=/scratch/local2/$PKG-$VERSION-$BUILD ; fi | ||
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| PATH=/bin:/usr/bin:/usr/sbin:/usr/local/bin | ||
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| set -eu | ||
| umask 022 | ||
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| BUILD_TMPDIR=/scratch/local2/$PKG-$VERSION-$BUILD.$USER.build.tmp | ||
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| test -d $BUILD_TMPDIR && ( chmod -R u+rwx $BUILD_TMPDIR || true ; rm -rf $BUILD_TMPDIR ) | ||
| export TMPDIR=$BUILD_TMPDIR | ||
| export HOME=$BUILD_TMPDIR/home | ||
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| exec </dev/null | ||
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| mkdir -p $PREFIX | ||
| cat >$PREFIX/profile <<-EOF | ||
| # pymol is build with current system python-3.12.8-0, if it is phased out, source it ... | ||
| PYFP='3.12.8.*Jan 6 2025, 13:15:47' | ||
| python -VV | grep -q "\$PYFP" || . /pkg/python-3.12.8-0/profile | ||
| PATH=$PREFIX/bin:\$PATH | ||
| export LD_LIBRARY_PATH=$PREFIX/lib\${LD_LIBRARY_PATH:+:\$LD_LIBRARY_PATH} | ||
| PKG_CONFIG_PATH=$PREFIX/lib/pkgconfig\${PKG_CONFIG_PATH:+:\$PKG_CONFIG_PATH} | ||
| export PKG_CONFIG_PATH | ||
| if [ -d $PREFIX/.compatlibs ]; then export LD_LIBRARY_PATH=$PREFIX/.compatlibs\${LD_LIBRARY_PATH:+:\$LD_LIBRARY_PATH} ; fi | ||
| EOF | ||
| . $PREFIX/profile | ||
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| NPROC=$(( $(nproc) * 4 / 5 + 1 )) | ||
| export MAKEFLAGS="-j $NPROC" | ||
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| BUILDDIR=$PREFIX/build | ||
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| mkdir -p $BUILDDIR | ||
| cd $BUILDDIR | ||
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| if /bin/true ; then | ||
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| ( | ||
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| # orig: https://github.com/msgpack/msgpack-c/archive/refs/tags/cpp-6.1.1.tar.gz | ||
| BEEHIVE=https://beehive.molgen.mpg.de/a0398798d8b9733bd5cd87a6d2f0b05f/msgpack-c-cpp-6.1.1.tar.gz | ||
| test -e msgpack-c-cpp-6.1.1.tar.gz || wget -nv $BEEHIVE | ||
| test -d msgpack-c-cpp-6.1.1 || tar -xf msgpack-c-cpp-6.1.1.tar.gz | ||
| cd msgpack-c-cpp-6.1.1 | ||
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| mkdir -p build | ||
| cd build | ||
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| cmake \ | ||
| -DCMAKE_BUILD_TYPE=Release \ | ||
| -DCMAKE_INSTALL_PREFIX=$PREFIX \ | ||
| -DCMAKE_VERBOSE_MAKEFILE=ON \ | ||
| .. | ||
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| make -j $NPROC | ||
| make install | ||
| ) | ||
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| ( | ||
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| # orig: https://github.com/rcsb/mmtf-cpp/archive/refs/tags/v1.1.0.tar.gz | ||
| BEEHIVE=https://beehive.molgen.mpg.de/ec961ff406a1636b4c5a25de7d9bd47b/mmtf-cpp-1.1.0.tar.gz | ||
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| test -e mmtf-cpp-1.1.0.tar.gz || wget -nv $BEEHIVE | ||
| test -d mmtf-cpp-1.1.0 || tar -xf mmtf-cpp-1.1.0.tar.gz | ||
| cd mmtf-cpp-1.1.0 | ||
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| mkdir -p build | ||
| cd build | ||
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| cmake \ | ||
| -DCMAKE_BUILD_TYPE=Release \ | ||
| -DCMAKE_INSTALL_PREFIX=$PREFIX \ | ||
| -DCMAKE_VERBOSE_MAKEFILE=ON \ | ||
| -DCMAKE_PREFIX_PATH=$PREFIX \ | ||
| .. | ||
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| make -j $NPROC | ||
| make install | ||
| ) | ||
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| ( | ||
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| # orig: https://github.com/g-truc/glm/archive/refs/tags/1.0.1.tar.gz | ||
| BEEHIVE=https://beehive.molgen.mpg.de/f824ac50e16310a95279032f82cbd341/glm-1.0.1.tar.gz | ||
| test -e glm-1.0.1.tar.gz || wget -nv $BEEHIVE | ||
| test -d glm-1.0.1 || tar -xf glm-1.0.1.tar.gz | ||
| cd glm-1.0.1 | ||
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| mkdir -p build | ||
| cd build | ||
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| cmake \ | ||
| -DCMAKE_BUILD_TYPE=Release \ | ||
| -DCMAKE_INSTALL_PREFIX=$PREFIX \ | ||
| -DCMAKE_VERBOSE_MAKEFILE=ON \ | ||
| -DCMAKE_PREFIX_PATH=$PREFIX \ | ||
| -DGLM_TEST_ENABLE=OFF \ | ||
| .. | ||
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| make -j $NPROC | ||
| mkdir -p $PREFIX/include | ||
| cp -ax ../glm $PREFIX/include | ||
| ) | ||
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| fi | ||
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| ( | ||
| # orig: https://github.com/schrodinger/pymol-open-source/archive/refs/tags/v3.1.0.tar.gz | ||
| BEEHIVE=https://beehive.molgen.mpg.de/459f483231e1d521824b0e74df5ba640/pymol-open-source-3.1.0.tar.gz | ||
| test -e pymol-open-source-3.1.0.tar.gz || wget -nv $BEEHIVE | ||
| test -d pymol-open-source-3.1.0 || tar -xf pymol-open-source-3.1.0.tar.gz | ||
| cd pymol-open-source-3.1.0 | ||
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| # patch setup.py, great, everthing else but a hack is a waste of time ... | ||
| # needed -lcurl -lhdf5_hl -lhdf5_cpp -lhdf5, hdf 5 is static, curl was forgotten ? | ||
| # old: extra_link_args = ext_link_args, | ||
| # new: extra_link_args = ['-lcurl', '-lhdf5_hl', '-lhdf5_cpp', '-lhdf5'] + ext_link_args, | ||
| sed -i -e '/\s\s*extra_link_args/ s/= /= \["-lcurl", "-lhdf5_hl", "-lhdf5_cpp", "-lhdf5"\] + /' setup.py | ||
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| export PREFIX_PATH=$PREFIX | ||
| export CXXFLAGS='-I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2' | ||
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| python setup.py build --use-msgpackc c++11 | ||
| python setup.py install --prefix=$PREFIX | ||
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| # autsch ... | ||
| sed -i -e "s|/pkg/python-3.12.8-0/lib|$PREFIX/lib|" $PREFIX/bin/pymol | ||
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| ) | ||
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