Hi RDKitters (in particular Hans), I have an issue with the installation of the RDKit postgres cartridge using the brewed version of RDKit. I got an email from Eddie yesterday (below) with some instruction from Hans about how to do it. However I'm experiencing some problems.
My issue starts at step 2) (it's worth noting that I'm doing this with the latest release of RDKit). I started by following the instructions as they were but when I got to the make stage I get the error below, adapter.cpp:32:10: fatal error: 'GraphMol/RDKitBase.h' file not found #include <GraphMol/RDKitBase.h> So I then went back and checked a few things and it seems that my $RDBASE variable is in a different place to the instructions mine is /usr/local/share/RDKit I then created the link from the source to this RDBASE and I get the same error when I try to make. This is about where my knowledge of UNIX runs out, so I thought I should ask the forum before I end up breaking it all! Thanks in advance. Best, Nick Nicholas C. Firth | PhD Student | Cancer Therapeutics The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | Surrey | SM2 5NG T 020 8722 4033 | E [email protected]<mailto:[email protected]> | W www.icr.ac.uk<http://www.icr.ac.uk/> | Twitter @ICRnews<https://twitter.com/ICRnews> Facebook www.facebook.com/theinstituteofcancerresearch<http://www.facebook.com/theinstituteofcancerresearch> Making the discoveries that defeat cancer [cid:[email protected]] Begin forwarded message: From: Yiqun Cao <[email protected]<mailto:[email protected]>> Subject: Re: PostGres cartridge Date: 14 May 2013 06:51:08 BST To: Nicholas Firth <[email protected]<mailto:[email protected]>> Hi Nick, The Homebrew formula does not install PostgreSQL cartridge. However, almost a year ago, Hans De Winter sent me an email detailing how he got it to work. I was supposed to turn that into new capability of the formula, but it's never happened... Anyway, here is the email and I hope you find it useful. (Someday I will update the formula properly... I still get to dream :)) Eddie Eddie, It seems I managed to get it working. These are the steps that I needed to do (I hope to be as accurate as possible; it also assumes that RDKit has been installed with your Homebrew recipe): 1) Installation of PostgreSQL - Download postgresql-9.1.3.tar.gz from http://www.postgresql.org/ftp/source/v9.1.3/ and uncompressed the contents into /usr/local/src. Install according the documentation provided by PostgreSQL: > cd /usr/local/src/postgresql-9.1.3/ > mkdir build > cd build > ../configure > make world > make check > sudo make install-world - Update my ~/.bash_profile to include the following: export PATH="$PATH:/usr/local/pgsql/bin" export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:/usr/local/pgsql/lib" export PGDATA="/usr/local/pgsql/data" 2) Install the cartridge Start by downloading the source code of RDKit (version 2012.03.1) and install it under /usr/local/src. Start the installation by creating a link from the source code into /usr/local/Cellar: > cd /usr/local/Cellar/rdkit/2012.03.1 > ln -s /usr/local/src/RDKit_2012_03_1/Code Make sure that the following environment variables are defined (I'm not sure all of these are required): export RDBASE="/usr/local/Cellar/rdkit/2012.03.1" export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$RDBASE/lib" export PYTHONPATH="$PYTHONPATH:/usr/local/lib/python2.7/site-packages" Chdir into /usr/local/src/RDKit_2012_03_1/Code/PgSQL/rdkit and remove the 'static linking' directive from the Makefile by replacing the 3rd line (STATIC_LINK=1) into 'STATIC_LINK=0'. Then start the installation: > make > sudo make install 3) Install the extension Assuming you have installed a PostgreSQL user (should be a superuser and the here described steps might be less 'accurate' since I'm not remembering exactly how I managed this), one can install the extension from within psql: > psql => create extension "rdkit"; CREATE EXTENSION => show rdkit.tanimoto_threshold; rdkit.tanimoto_threshold -------------------------- 0.5 (1 row) => select 'c1ccccc1O'::mol; mol ----------- Oc1ccccc1 (1 row) I hope these steps might help you in creating a Homebrew formula to install the PostgreSQL cartridge? Please ask if you need more info or a helping hand... Cheers, Hans The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
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