Bioscape Installation

Note	Please note that this documentation covers an unreleased product and is for internal use only.

Installation

Bioscape consists of three separate applications which must be combined to provide all the facilities of a functional Bioscape installation:

• The administrative application: bsadmin
• The text-indexing application: bsindex
• The Web front-end application: bsweb

Before installing, it is necessary to consider the dependencies listed in the section given below. Precise information about installing the dependencies is not provided in this document, and it is recommended that you make use of your system's package management tools, perhaps installing Bioscape itself from suitable packages, in order to save time and effort working through the installation process manually. However, for those interested in installing Bioscape from the source code distribution of each application, the procedure is given below.

Installation from Source Code

First, nominate a common directory to hold the Bioscape application directories. For example:

/home/bioscape/apps

Then, acquire each application's source code distribution (details to be provided) and unpack the archives in this common directory:

cd /home/bioscape/apps
tar zxf bsadmin-x.y.tar.gz
tar zxf bsindex-x.y.tar.gz
tar zxf bsweb-x.y.tar.gz

Since these applications contain Python libraries, it is important to configure the environment so that they may be accessed by Python. This may be done by creating a short configuration file resembling the one provided as docs/configuration/env.sh in the bsadmin distribution and then incorporating it into your environment within a .bashrc or equivalent file as follows:

source /home/bioscape/apps/bsadmin/docs/configuration/env.sh

Installation of Dependencies

See the Bioscape Dependencies page for a list of the dependencies.

The docs/dependencies/download.sh file in the bsadmin distribution provides some commands which should be able to download the source distributions of various dependencies. This file or a modified version of it could be run in a nominated directory which would then hold copies of the dependencies' archive files.

The docs/dependencies/build.sh file in the bsadmin distribution provides some commands which could be run to build each of the dependencies from the previously downloaded archive files.

For some of the dependencies, even with pre-installed packages, you will need to do some preparatory work in order to use Bioscape. This is documented on the Bioscape Configuration page.