5 ms·

most commonly rdkit, where I've never managed to build all the dependencies

by fock 5y ago

navanchauhan 5y ago
I agree. So many times I have had to reinstall rdkit using homebrew and link it again and again. Although, you can now install rdkit via pip: pip install rdkit-pypi GitHub Issue: https://github.com/rdkit/rdkit/issues/1812#issuecomment-808810574 https://github.com/rdkit/rdkit/issues/1812#issuecomment-8088...
dalke 5y ago
For what it's worth, I have multiple RDKit instances on my Mac, so I can test chemfp against different toolkit releases. It's a headache! Here's my notes from installation - I have to keep notes as hints for newer releases: /Users/dalke/local/bin/python3.9 -m venv ~/venvs/py39-2021-4 source ~/venvs/py39-2021-4/bin/activate.csh pip install numpy scipy matplotlib pandas cd ~/ftps tar xf Release_2021_03_1.tar.gz cd rdkit-Release_2021_03_1 mkdir build_py39-2021-4 cd build_py39-2021-4/ cmake .. -DRDK_INSTALL_INTREE=OFF \ -DCMAKE_INSTALL_PREFIX=/Users/dalke/venvs/py39-2021-4 \ -DCMAKE_INSTALL_RPATH="/Users/dalke/venvs/py39-2021-4/lib/;/Users/dalke/local/lib/" \ -DRDK_BUILD_AVALON_SUPPORT=ON \ -DRDK_BUILD_CAIRO_SUPPORT=ON \ -DRDK_BUILD_INCHI_SUPPORT=ON \ -DRDK_BUILD_COMPRESSED_SUPPLIERS=ON make -j4 make install and then manual edit (!) activate.csh so the DYLD_LIBRARY_PATH is updated: alias deactivate 'test $?_OLD_VIRTUAL_PATH != 0 && setenv PATH "$_OLD_VIRTUAL_PATH" && unset _OLD_VIRTUAL_PATH && setenv DYLD_LIBRARY_PATH "$_OLD_DYLD_LIBRARY_PATH" && unset _OLD_DYLD_LIBRARY_PATH; rehash; test $?_OLD_VIRTUAL_PROMPT != 0 && set prompt="$_OLD_VIRTUAL_PROMPT" && unset _OLD_VIRTUAL_PROMPT; unsetenv VIRTUAL_ENV; test "\!:*" != "nondestructive" && unalias deactivate' ... if (`printenv DYLD_LIBRARY_PATH` == '') then set _OLD_DYLD_LIBRARY_PATH="" setenv DYLD_LIBRARY_PATH "$VIRTUAL_ENV/lib" else set _OLD_DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH" setenv DYLD_LIBRARY_PATH "$VIRTUAL_ENV/lib:$DYLD_LIBRARY_PATH" endif You'll note that I'm a tcsh user ('cause that was kewl in the 1990s when I started in Unix) and my directory structure uses "~/ftps" for things I've manually downloaded (ditto), and I'm probably using venv poorly. Oh, but am I done? No! See the "/Users/dalke/local/lib/" in the CMAKE_INSTALL_RPATH? That's because I installed my own Python, and Boost: cd ~/ftps curl -O 'https://www.python.org/ftp/python/3.9.1/Python-3.9.1.tar.xz' tar xf Python-3.9.1.tar.xz cd Python-3.9.1 ./configure --prefix ~/local --with-openssl=/usr/local/opt/openssl make -j3 make install cd ~/ftps tar xf boost_1_72_0.tar.gz cd boost_1_72_0 ./bootstrap.sh --prefix=/Users/dalke/local --with-python=/Users/dalke/local/bin/python3.9 --with-toolset=clang --with-python-version=3.9 ./b2 -j 4 ./b2 install And even then it's a house of cards that will likely collapse when I install python 3.10. Oh, and I have multiple Open Babel installs from scratch, for the same reasons Pity me. :)
physicsguy 5y ago
Informatics pipeline software in general seem to be "All that accepted practice about distributing software? Let's throw it out of the window"

most commonly rdkit, where I've never managed to build all the dependencies

by fock 5y ago

most commonly rdkit, where I've never managed to build all the dependencies

I agree. So many times I have had to reinstall rdkit using homebrew and link it again and again. Although, you can now install rdkit via pip: pip install rdkit-pypi GitHub Issue: https://github.com/rdkit/rdkit/issues/1812#issuecomment-808810574 https://github.com/rdkit/rdkit/issues/1812#issuecomment-8088...

dalke 5y ago

For what it's worth, I have multiple RDKit instances on my Mac, so I can test chemfp against different toolkit releases. It's a headache! Here's my notes from installation - I have to keep notes as hints for newer releases: /Users/dalke/local/bin/python3.9 -m venv ~/venvs/py39-2021-4 source ~/venvs/py39-2021-4/bin/activate.csh pip install numpy scipy matplotlib pandas cd ~/ftps tar xf Release_2021_03_1.tar.gz cd rdkit-Release_2021_03_1 mkdir build_py39-2021-4 cd build_py39-2021-4/ cmake .. -DRDK_INSTALL_INTREE=OFF \ -DCMAKE_INSTALL_PREFIX=/Users/dalke/venvs/py39-2021-4 \ -DCMAKE_INSTALL_RPATH="/Users/dalke/venvs/py39-2021-4/lib/;/Users/dalke/local/lib/" \ -DRDK_BUILD_AVALON_SUPPORT=ON \ -DRDK_BUILD_CAIRO_SUPPORT=ON \ -DRDK_BUILD_INCHI_SUPPORT=ON \ -DRDK_BUILD_COMPRESSED_SUPPLIERS=ON make -j4 make install and then manual edit (!) activate.csh so the DYLD_LIBRARY_PATH is updated: alias deactivate 'test $?_OLD_VIRTUAL_PATH != 0 && setenv PATH "$_OLD_VIRTUAL_PATH" && unset _OLD_VIRTUAL_PATH && setenv DYLD_LIBRARY_PATH "$_OLD_DYLD_LIBRARY_PATH" && unset _OLD_DYLD_LIBRARY_PATH; rehash; test $?_OLD_VIRTUAL_PROMPT != 0 && set prompt="$_OLD_VIRTUAL_PROMPT" && unset _OLD_VIRTUAL_PROMPT; unsetenv VIRTUAL_ENV; test "\!:*" != "nondestructive" && unalias deactivate' ... if (`printenv DYLD_LIBRARY_PATH` == '') then set _OLD_DYLD_LIBRARY_PATH="" setenv DYLD_LIBRARY_PATH "$VIRTUAL_ENV/lib" else set _OLD_DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH" setenv DYLD_LIBRARY_PATH "$VIRTUAL_ENV/lib:$DYLD_LIBRARY_PATH" endif You'll note that I'm a tcsh user ('cause that was kewl in the 1990s when I started in Unix) and my directory structure uses "~/ftps" for things I've manually downloaded (ditto), and I'm probably using venv poorly. Oh, but am I done? No! See the "/Users/dalke/local/lib/" in the CMAKE_INSTALL_RPATH? That's because I installed my own Python, and Boost: cd ~/ftps curl -O 'https://www.python.org/ftp/python/3.9.1/Python-3.9.1.tar.xz' tar xf Python-3.9.1.tar.xz cd Python-3.9.1 ./configure --prefix ~/local --with-openssl=/usr/local/opt/openssl make -j3 make install cd ~/ftps tar xf boost_1_72_0.tar.gz cd boost_1_72_0 ./bootstrap.sh --prefix=/Users/dalke/local --with-python=/Users/dalke/local/bin/python3.9 --with-toolset=clang --with-python-version=3.9 ./b2 -j 4 ./b2 install And even then it's a house of cards that will likely collapse when I install python 3.10. Oh, and I have multiple Open Babel installs from scratch, for the same reasons Pity me. :)

physicsguy 5y ago

Informatics pipeline software in general seem to be "All that accepted practice about distributing software? Let's throw it out of the window"