This is an attempt to modify myChEMBL so it can be used on an existing Mac OS X machine instead of a virtual machine.
Why? It's a nice way to quickly set up your own machine with a local copy of the ChEMBL database along with the associated chemistry toolkits, database software, web services and learning materials.
As this is intended to be run on an existing system instead of a virtual machine, there are some differences from myChEMBL:
- Instead of overwriting configuration files completely, the necessary changes are made to existing configuration files in an effort to preserve any other customisations you might already have.
- Instead of installing the myChEMBL launchpad and web app at the root level of the web server, files are installed to
~/Sites/mychembland are therefore accessible from
- For safety, the Apache web server, PostgreSQL server and iPython notebook server are all configured to only listen to localhost and ignore requests from elsewhere by default.
- As we are targeting OS X instead of Ubuntu, the homebrew package manager is used instead of
bootstrap.sh script hasn’t been widely tested, so please take a minute to read through and understand what it does before running it.
Added and modified files
- Homebrew installs packages in
- pip installs python packages to
- iPython notebooks are installed to
- myChEMBL launchpad is installed to
- myChEMBL web app is installed to
- ChEMBL web service Django app is installed to
- PostgreSQL configuration at
- The ChEMBL PostgreSQL database is stored at
Start/stop the Apache web server using
apachectl start and
Start/stop the PostgreSQL database using:
pg_ctl -D /usr/local/var/postgres -l /usr/local/var/postgres/server.log start pg_ctl -D /usr/local/var/postgres stop -s -m fast
You may want to create shortcuts for these in your
alias startpost='pg_ctl -D /usr/local/var/postgres -l /usr/local/var/postgres/server.log start' alias stoppost='pg_ctl -D /usr/local/var/postgres stop -s -m fast' alias restartpost='stoppost && sleep 1 && startpost'
View the iPython notebooks using:
ipython notebook --profile=mychembl
MyChEMBL web app
Visit the myChEMBL web app by going to
The web app files are at:
ChEMBL web services
Acess the ChEMBL web services by going to
The web services Django app is at