GCP - Bioinformatics - Web Services

[Welcome]

Select a computer to run TAPIR. The server wll have to be accessible via internet, so a public address must be assigned to it. This page lists system requirements and prerequisites.
Install Subversion version control system client. Packages and installers are available on this page.
Install the target database system. This doesn't mean that the database needs to reside on the same machine, although this configuration maximises communication speed with the database; but if you install, for instance MySQL or PostgreSQL, once you load needed components, the libraries that interact with the database will also be installed.
Determine TAPIR directory. The location of TAPIR depends on how you want to run it, there are two ways of running TAPIR: as a standalone server or behind a webserver via FastCGI, both procedures are described in the installation guide. If you wish to run it behind a web server, the location is dependant on your web configuration. In this summary we will describe the standalone server option, in this case the location is at your discretion.
Download the software. Open a terminal and position in the directory that will contain TAPIR. Type the following command:
svn co svn://svn.pywrapper.org:80/pywrapper/branches/stable pywrapper (all in one line)
This command will create a directory called pywrapper which will contain all files needed by TAPIR.
Load needed components. In the previous step all the specific TAPIR elements have been installed in the pywrapper directory, but the support elements, such as Python and the required libraries, are missing. To install these you need first to go in the tools directory:
cd pywrapper/tools
Then you need to install the libraries:
./install.sh
Depending on the speed of your server you may have enough time to take a coffee.
Run the TAPIR server. The last lines of the terminal will indicate the command needed to run TAPIR:
../webapp/start_server.py 8080
Where 8080 indicates on which port you wish to start the server, if you have other services running on the server you must use a free port. Note that web uses 80 and Tomcat uses 8080.

Point your web browser to your TAPIR server. Typically, you will do this on the same machine that runs TAPIR, for the first time, thereafter you will do it by accessing the public address. You will get the home page.
Enter main configuration. The first thing you should do is set the main configuration settings. Press on ConfigTool and select the general system options link. You will be asked to put a password: the default one is ACDC. You will then get the system configuration form.
Change system configuration password. Since your server is accessible from the internet it is a good idea to change the system configuration password.
Set the host domain. This is the base domain from which your server will be accessed. Change the base URL to match your domain and set the used port.
Set the base URL. This is the last portion of the URL by which you access TAPIR, in the current example it would be http://localhost:8081/pywrapper. Note that you can leave it unchanged.
Set the Graphviz dot binary. This is the optional path to the dot binaries that are used to draw database structures, if you don't have it, just clear the field.
Save Server settings.
Add GCP concept name server. You should set http://generationcp.org/schemas/alias.txt as Secondary CNS. This will ensure you have latest GCP schemas and MOBY templates available.
Save concept name servers.

Subprogramme Leader Theo van Hintum, Wageningen,
theo.vanhintum@wur.nl