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Cheminformatics formulae for the Homebrew package manager

Ruby 100.00%

homebrew cheminformatics packages formulae ruby science

homebrew-cheminformatics's Introduction

homebrew-cheminformatics

Cheminformatics formulae for the Homebrew package manager.

Instructions

Homebrew must be installed:

ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"
brew update
brew doctor

Add this cheminformatics tap:

brew tap mcs07/cheminformatics

Install what you want:

brew install cdk
brew install filter-it
brew install helium
brew install indigo
brew install inchi
brew install opsin
brew install osra
brew install rdkit
...

Look in the Formula directory for a full list of what is available.

Options

Use brew info to see information and all the available options for a formula:

brew info rdkit

Most options are to enable optional features that have extra dependencies or to include additional language bindings for Python and Java.

For many formulae, there is also a --HEAD option to install the latest cutting edge development master.

Open Babel

There is already an Open Babel formula in the main homebrew repository. To use the formula in this tap, you will need to specify the full path:

brew install mcs07/cheminformatics/open-babel

The formulae are very similar. The main difference is that the formula in this tap installs Open Babel in a way that won't clash with other tools that also depend on the InChI library.

RDKit and Python 3

RDKit can be built to work with either Python 2 or Python 3, but not both simultaneously. The default is Python 2. For Python 3 support, use the --with-python3 option.

RDKit can have trouble finding the correct boost-python3 libraries. If you get errors installing RDKit, consider installing boost-python without support for python 2:

brew install boost-python --without-python --with-python3
brew install rdkit --HEAD --with-python3

RDKit and virtualenvs

RDKit does not play nice with virtual environments. Running brew install rdkit while inside a virtualenv tends not to work properly. To install RDKit in a a virtual environment:

Run brew install rdkit outside a virtualenv. This will install everything to /usr/local/Cellar/rdkit, and RDKit should work in your main python install outside a virtualenv.
Copy the contents of /usr/local/Cellar/rdkit/20XX.XX.X/lib/python2.7/site-packages to ~/.virtualenvs/<env>/lib/python2.7/site-packages. RDKit should then work within that virtualenv.

Every time you update RDKit or python, you will probably have to repeat this process. Not great, but it works.

Feedback and requests

Please add any requests for a new formula or bug reports to the Github issue tracker. Alternatively, email me at [email protected].

homebrew-cheminformatics's People

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Forkers

abhik1368 greatlse kl3ryk corykornowicz

homebrew-cheminformatics's Issues

Depreciated calls in Homebrew 1.5.10

Hi,
I'm receiving some warnings in homebrew about depreciated calls during brew update

Warning: Calling 'depends_on :python' is deprecated!
Use 'depends_on "python@2"' instead.
/usr/local/Homebrew/Library/Taps/mcs07/homebrew-cheminformatics/Formula/indigo.rb:21:in `class:Indigo'
Please report this to the mcs07/cheminformatics tap!

Warning: Calling 'depends_on :python3' is deprecated!
Use 'depends_on "python"' instead.
/usr/local/Homebrew/Library/Taps/mcs07/homebrew-cheminformatics/Formula/open-babel.rb:18:in `class:OpenBabel'
Please report this to the mcs07/cheminformatics tap!

Warning: Calling 'depends_on :postgresql' is deprecated!
Use 'depends_on "postgresql"' instead.
/usr/local/Homebrew/Library/Taps/mcs07/homebrew-cheminformatics/Formula/rdkit.rb:32:in `class:Rdkit'
Please report this to the mcs07/cheminformatics tap!

I think it has to do with some changes to the way homebrew handles the different python versions now.

Any help would be appreciated and let me know if you need any more information from me.

-David

osra installer failed + update to osra 2.0.1 version

$ brew install osra
==> Installing osra from mcs07/cheminformatics
==> Installing dependencies for mcs07/cheminformatics/osra: graphicsmagick
==> Installing mcs07/cheminformatics/osra dependency: graphicsmagick
==> Downloading https://homebrew.bintray.com/bottles/graphicsmagick-1.3.23_1.el_capitan.bottle.tar.gz
Already downloaded: /Library/Caches/Homebrew/graphicsmagick-1.3.23_1.el_capitan.bottle.tar.gz
==> Pouring graphicsmagick-1.3.23_1.el_capitan.bottle.tar.gz
🍺 /usr/local/Cellar/graphicsmagick/1.3.23_1: 471 files, 11.8M
==> Installing mcs07/cheminformatics/osra
==> Downloading https://downloads.sourceforge.net/project/osra/osra/2.0.0/osra-2.0.0.tgz
Already downloaded: /Library/Caches/Homebrew/osra-2.0.0.tgz
==> ./configure --prefix=/usr/local/Cellar/osra/2.0.0
==> make
Last 15 lines from /Users/mbp/Library/Logs/Homebrew/osra/02.make:
^
osra_grayscale.cpp:274:17: error: call to member function 'adaptiveThreshold' is ambiguous
image.adaptiveThreshold(window,window,7);
~~~~~~^~~~~~~~~~~~~~~~~
/usr/local/Cellar/graphicsmagick/1.3.23_1/include/GraphicsMagick/Magick++/Image.h:116:21: note: candidate function
void adaptiveThreshold ( const unsigned int width,
^
/usr/local/Cellar/graphicsmagick/1.3.23_1/include/GraphicsMagick/Magick++/Image.h:119:21: note: candidate function
void adaptiveThreshold ( const unsigned int width,
^
2 errors generated.
make[2]: *** [osra_grayscale.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [all] Error 2
make: *** [all.subdir] Error 2

Can we have the 2.0.1 version also in the tap ?

CMake issue on OSRA install: InChI library not found

Hi,

In going through the recommended brew packages as per https://www.macinchem.org/reviews/cheminfo/cheminfoMacUpdate.php, I've run into the following error:

brew install osra
==> Installing osra from mcs07/cheminformatics
==> Installing dependencies for mcs07/cheminformatics/osra: mcs07/cheminformatics/open-babel, libtool and graphicsmagick
==> Installing mcs07/cheminformatics/osra dependency: mcs07/cheminformatics/open-babel
==> Downloading https://github.com/openbabel/openbabel/archive/openbabel-2-4-1.tar.gz
Already downloaded: /Users/davidpolefrone/Library/Caches/Homebrew/downloads/6937db17b0d685087dbefb2a69072e743cba78cd3001a51e8f29c1fbcea06e67--openbabel-openbabel-2-4-1.tar.gz
==> cmake .. -DOPENBABEL_USE_SYSTEM_INCHI=ON
Last 15 lines from /Users/davidpolefrone/Library/Logs/Homebrew/open-babel/01.cmake:
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++
-- Check for working CXX compiler: /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Could NOT find INCHI (missing: INCHI_LIBRARY INCHI_INCLUDE_DIR)
CMake Error at CMakeLists.txt:151 (message):
Inchi library not found.

-- Configuring incomplete, errors occurred!
See also "/tmp/open-babel-20200321-32477-145s3aq/openbabel-openbabel-2-4-1/build/CMakeFiles/CMakeOutput.log".

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/mcs07/homebrew-cheminformatics/issues

How can this configuration error be fixed?

CMake error while installing Indigo

Based on the error below - would I need to upgrade my CMake version to get around this error? (the log file is empty)
Thanks for advise!

justins-mbp-3:5.0.20180306 jjjvanderhooft$ brew install indigo
==> Installing indigo from mcs07/cheminformatics
==> Downloading https://github.com/epam/Indigo/archive/indigo-1.3.0beta.tar.gz
Already downloaded: /Users/jjjvanderhooft/Library/Caches/Homebrew/indigo-1.3.0-beta.tar.gz
==> cmake ../build_scripts/indigo-all
Last 15 lines from /Users/jjjvanderhooft/Library/Logs/Homebrew/indigo/01.cmake:
-- Check for working CXX compiler: /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++
-- Check for working CXX compiler: /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Error at /tmp/indigo-20180724-50492-1mah2ic/Indigo-indigo-1.3.0beta/common/cmake/GetSystemVersion.cmake:35 (message):
Unsupported DARWIN_VERSION: 17
Call Stack (most recent call first):
/tmp/indigo-20180724-50492-1mah2ic/Indigo-indigo-1.3.0beta/common/cmake/ConfigureCommon.cmake:5 (include)
CMakeLists.txt:9 (INCLUDE)

-- Configuring incomplete, errors occurred!
See also "/tmp/indigo-20180724-50492-1mah2ic/Indigo-indigo-1.3.0beta/build-lib/CMakeFiles/CMakeOutput.log".

Tap cannot be run because of error

Just tried to run the tap and go the following error

n00002621@CHEM-72061 ~ % brew tap mcs07/cheminformatics
==> Tapping mcs07/cheminformatics
Cloning into '/usr/local/Homebrew/Library/Taps/mcs07/homebrew-cheminformatics'...
remote: Enumerating objects: 1040, done.
remote: Total 1040 (delta 0), reused 0 (delta 0), pack-reused 1040
Receiving objects: 100% (1040/1040), 159.27 KiB | 1.03 MiB/s, done.
Resolving deltas: 100% (480/480), done.
Error: Invalid formula: /usr/local/Homebrew/Library/Taps/mcs07/homebrew-cheminformatics/Formula/osra.rb
osra: Calling depends_on :java is disabled! Use "depends_on "openjdk@11", "depends_on "openjdk@8" or "depends_on "openjdk" instead.
Please report this issue to the mcs07/cheminformatics tap (not Homebrew/brew or Homebrew/core), or even better, submit a PR to fix it:
  /usr/local/Homebrew/Library/Taps/mcs07/homebrew-cheminformatics/Formula/osra.rb:16

Please help!

RDKit for python 2 and 3, both?

In the description of the rdkit formula it says "RDKit can be built to work with either Python 2 or Python 3, but not both simultaneously". I use both Python 2 and 3 from time to time, and it would be nice to have to not switch installations all the time. Is this a hard and fast rule or might there be a way around it?

Troubles with rdkit on MacOS 10.12.4

Installation for python 3 worked perfectly:

brew install --with-python3 rdkit

but installation for python 2 failed:

brew uninstall -f rdkit
brew install rdkit

Last 15 lines from /Users/andreas/Library/Logs/Homebrew/rdkit/02.make:
/usr/bin/ar qc libRDInchiLib_static.a  CMakeFiles/RDInchiLib_static.dir/inchi.cpp.o
/usr/bin/ranlib libRDInchiLib_static.a
[  2%] Built target RDInchiLib_static
[  2%] Linking CXX shared library ../../lib/libRDGeneral.dylib
cd /tmp/rdkit-20170429-33867-18zdqrb/rdkit-Release_2016_09_4/Code/RDGeneral && /usr/local/Cellar/cmake/3.8.0/bin/cmake -E cmake_link_script CMakeFiles/RDGeneral.dir/link.txt --verbose=1
/usr/local/Homebrew/Library/Homebrew/shims/super/clang++  -mpopcnt -std=c++11 -stdlib=libc++ -Wall -Wextra -Wno-unused-local-typedef -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -DNDEBUG -dynamiclib -Wl,-headerpad_max_install_names -compatibility_version 1.0.0 -current_version 2016.9.4 -o ../../lib/libRDGeneral.2016.09.4.dylib -install_name /tmp/rdkit-20170429-33867-18zdqrb/rdkit-Release_2016_09_4/lib/libRDGeneral.1.dylib CMakeFiles/RDGeneral.dir/Invariant.cpp.o CMakeFiles/RDGeneral.dir/types.cpp.o CMakeFiles/RDGeneral.dir/utils.cpp.o CMakeFiles/RDGeneral.dir/RDLog.cpp.o CMakeFiles/RDGeneral.dir/Dict.cpp.o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o CMakeFiles/RDGeneral.dir/versions.cpp.o /usr/local/lib/libboost_thread-mt.dylib /usr/local/lib/libboost_system-mt.dylib /usr/local/lib/libboost_thread-mt.dylib /usr/local/lib/libboost_system-mt.dylib 
cd /tmp/rdkit-20170429-33867-18zdqrb/rdkit-Release_2016_09_4/Code/RDGeneral && /usr/local/Cellar/cmake/3.8.0/bin/cmake -E cmake_symlink_library ../../lib/libRDGeneral.2016.09.4.dylib ../../lib/libRDGeneral.1.dylib ../../lib/libRDGeneral.dylib
[  2%] Built target RDGeneral
[  2%] Linking CXX static library libRDGeneral_static.a
cd /tmp/rdkit-20170429-33867-18zdqrb/rdkit-Release_2016_09_4/Code/RDGeneral && /usr/local/Cellar/cmake/3.8.0/bin/cmake -P CMakeFiles/RDGeneral_static.dir/cmake_clean_target.cmake
cd /tmp/rdkit-20170429-33867-18zdqrb/rdkit-Release_2016_09_4/Code/RDGeneral && /usr/local/Cellar/cmake/3.8.0/bin/cmake -E cmake_link_script CMakeFiles/RDGeneral_static.dir/link.txt --verbose=1
/usr/bin/ar qc libRDGeneral_static.a  CMakeFiles/RDGeneral_static.dir/Invariant.cpp.o CMakeFiles/RDGeneral_static.dir/types.cpp.o CMakeFiles/RDGeneral_static.dir/utils.cpp.o CMakeFiles/RDGeneral_static.dir/RDLog.cpp.o CMakeFiles/RDGeneral_static.dir/Dict.cpp.o CMakeFiles/RDGeneral_static.dir/LocaleSwitcher.cpp.o CMakeFiles/RDGeneral_static.dir/versions.cpp.o
/usr/bin/ranlib libRDGeneral_static.a
[  2%] Built target RDGeneral_static
make: *** [all] Error 2

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/mcs07/homebrew-cheminformatics/issues

Looking at the gist log

brew gist-logs rdkit

shows the following (https://gist.github.com/anonymous/54edc245bc38d5572be49f23675a4e86):

...
cd /tmp/rdkit-20170428-50140-10loi4b/External/INCHI-API && /usr/local/Homebrew/Library/Homebrew/shims/super/clang++  -DBUILD_INCHI_SUPPORT -DRDK_64BIT_BUILD -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/local/include/inchi -I/usr/local/Cellar/python/2.7.12_2/Frameworks/Python.framework/Versions/2.7/include/python2.7 -I/usr/local/lib/python2.7/site-packages/numpy/core/include -isystem /usr/local/include -I/tmp/rdkit-20170428-50140-10loi4b/Code -I/usr/local/include/eigen3  -mpopcnt -std=c++11 -stdlib=libc++ -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -DNDEBUG   -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/RDInchiLib_static.dir/inchi.cpp.o -c /tmp/rdkit-20170428-50140-10loi4b/External/INCHI-API/inchi.cpp
In file included from /tmp/rdkit-20170428-50140-10loi4b/Code/RDBoost/Wrap.cpp:16:
In file included from /tmp/rdkit-20170428-50140-10loi4b/Code/RDBoost/Wrap.h:19:
In file included from /usr/local/include/boost/python.hpp:11:
In file included from /usr/local/include/boost/python/args.hpp:8:
In file included from /usr/local/include/boost/python/detail/prefix.hpp:13:
/usr/local/include/boost/python/detail/wrap_python.hpp:50:11: fatal error: 'pyconfig.h' file not found
# include <pyconfig.h>
...

This is very curious, because the file "pyconfig.h" exists within /usr/local/Cellar/python/2.7.12_2/Frameworks/Python.framework/Versions/2.7/include/python2.7, which is listed as one of the -I flags to clang.

What worked for me was to create symlinks for all the files in /usr/local/Cellar/python/2.7.12_2/Frameworks/Python.framework/Versions/2.7/include/python2.7 in /usr/local/include, but this is hardly a good fix.

is your brew formula for rdkit better than the "official one"?

I'd be interested into something that installs more automatically.

issue installing indigo

Setting up a new mac with homebrew-cheminformatics

When I brew install indigo I get the following error:

==> Installing indigo from mcs07/cheminformatics
==> Installing dependencies for mcs07/cheminformatics/indigo: cmake
==> Installing mcs07/cheminformatics/indigo dependency: cmake
==> Downloading https://homebrew.bintray.com/bottles/cmake-3.7.1.el_capitan.bott
######################################################################## 100.0%
==> Pouring cmake-3.7.1.el_capitan.bottle.tar.gz
==> Caveats
Emacs Lisp files have been installed to:
/usr/local/share/emacs/site-lisp/cmake
==> Summary
🍺 /usr/local/Cellar/cmake/3.7.1: 2,143 files, 29M
==> Installing mcs07/cheminformatics/indigo
==> Downloading https://github.com/epam/Indigo/archive/indigo-1.2.1.tar.gz
==> Downloading from https://codeload.github.com/epam/Indigo/tar.gz/indigo-1.2.1
######################################################################## 100.0%
==> Downloading https://gist.githubusercontent.com/mcs07/b9b2ccfdb9bc23f60044/ra
######################################################################## 100.0%
==> Downloading https://gist.githubusercontent.com/mcs07/541bcda4cfd6a7d8668b/ra
######################################################################## 100.0%
==> Patching
==> Applying indigo-el-capitan.diff
patching file common/cmake/GetSystemVersion.cmake
patch unexpectedly ends in middle of line
Hunk #1 succeeded at 27 with fuzz 1.
==> Applying indigo-depict-1.2.1.diff
patching file utils/indigo-depict/CMakeLists.txt
==> cmake ../build_scripts/indigo-all
==> make
Last 15 lines from /Users/ebucholtz/Library/Logs/Homebrew/indigo/02.make:
Scanning dependencies of target indigo-inchi-c-test-shared
[ 99%] Building C object indigo-inchi/indigo-inchi/CMakeFiles/indigo-inchi-c-test-shared.dir/tests/c/indigo-inchi-test.c.o
[ 99%] Building C object indigo/api/CMakeFiles/indigo-c-test-shared.dir/tests/c/indigo-test.c.o
[ 99%] Linking CXX executable ../../dist/Mac/10.11/lib/indigo-inchi-c-test-shared
[ 99%] Linking CXX executable ../../dist/Mac/10.11/lib/indigo-c-test-shared
[ 99%] Built target indigo-renderer-shared
Scanning dependencies of target indigo-renderer-c-test-shared
make[2]: *** No rule to make target /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/System/Library/Frameworks/ApplicationServices.framework', needed by dist/Mac/10.11/lib/indigo-renderer-c-test-shared'. Stop.
make[2]: *** Waiting for unfinished jobs....
[ 99%] Building C object indigo-renderer/renderer/CMakeFiles/indigo-renderer-c-test-shared.dir/tests/c/indigo-renderer-test.c.o
[ 99%] Built target indigo-c-test-shared
make[1]: *** [indigo-renderer/renderer/CMakeFiles/indigo-renderer-c-test-shared.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 99%] Built target indigo-inchi-c-test-shared
make: *** [all] Error 2