Installation information

Preliminary note

Plone4bio has been developed so far on Linux, in particular on the  Debian and  Ubuntu distributions. While we do not expect major problems on other Linux distributions, be aware that installing on Windows and Mac OSX have not been performed before. We have preliminary instructions to InstallTheSoftwareonWindows (thanks to Jerry Black). Nonetheless installation should be possible on any system where Plone is supported (thus on Windows and MacOSX, too).

If you perform a successful installation on windows or MacOsX, please share the information.

Hardware requirements

Any reasonably recent machine capable of running Plone should do, however keep in mind that, at some point during indexing, Plone search engine has a relatively large need for RAM.

The  plone4bio demo site, that indexes human CDS entries from NCBI and human proteins from Uniprot, runs on a virtual machine with 4GB of RAM. Furthermore indexing it from scratch takes a couple of hours of time, so do not expect search to immediately work for databases with tens-of-thousands sequences (on the contrary browsing is immediately available) .

We have no hard number at the moment, but let'say that 4 GB of available RAM is a requirement to index a complete euchariotic genome. So do not do it on a netbook ;-)

Software requirements

  • python2.4
  • python2.4 development files (i.e. in Debian it is python2.4-dev)
  • python setuptools (please, be sure of having the latest setuptools available ---  http://pypi.python.org/pypi/setuptools/)
  • PIL (i.e. in Debian it is python-imaging)
  • on Debian you can issue: 
apt-get install python2.4 python2.4-dev python-imaging gcc python-setuptools make subversion python-subversion \
libc6-dev libcairo2-dev python-cairo libncurses5-dev libpq-dev python-sqlalchemy python-libxml2 python-lxml \
less libmysqlclient15-dev

Packages useful to index pdf and doc files: 

apt-get install poppler-utils wv

Then create a plone user: 

adduser plone
chown -R plone.plone /opt
su - plone

And as plone execute the following (N.B. all the relevant libraries, such as Biopython or Numpy, are installed by buildout):

Latest stable release (1.0)

cd /opt/
svn co https://www.plone4bio.org/svn/plone4bio.buildout/tags/1.0/ plone4bio.buildout
cd plone4bio.buildout
ln -s demo.cfg buildout.cfg
python2.4 bootstrap.py
bin/buildout -v

Development release (trunk)

cd /opt/
svn co https://www.plone4bio.org/svn/plone4bio.buildout/trunk/ plone4bio.buildout
cd plone4bio.buildout
ln -s demo.cfg buildout.cfg
python2.4 bootstrap.py
bin/buildout -v

To visualize the features you will also need to install Bioperl.