How to configure Wormbase Converter for use with the CIML server

Wormbase Converter was originally designed as part of an analysis package to enable lists of functional annotations used by the EASE program to be automatically kept up-to-date. Unfortunately, the stand-alone version of EASE provided by its developers only runs under Windows. For this reason, when Wormbase Converter was developed, most effort was put into making a user-friendly Windows version. If you have access to a PC, then this will be by far the easiest option for you!

1. Installing WormBase Converter Client on a PC

If you havenÕt already done so, download the Wormbase Converter from Sourceforge:

http://wormbasemanager.sourceforge.net/downloads/WBConverter__Client__Windows.zip.

Save the zip archive, then extract all the files. For the programme to run properly, you need to extract the archive into a folder on the ÒC:Ó drive, not just onto the desktop. There are very complete installation instructions in the file ÒDocumentation.pdfÓ in the Help folder. But briefly, after downloading and extracting, launch the ÒConfiguration WizardÓ.

Description: config.tiff

Enter Òhttp://www.ciml.univ-mrs.fr/applications/WB_converterÓ as the host address.

Then when you hit ÒTest the serverÓ, it should look like this:

Then hit ÒSAVE THIS CONFIGURATIONÓ.

ThatÕs all! You can now launch the application.

2. Installing WormBase Converter Client on a linux computer

 

To install the software under Linux, download the ÒSourcesÓ for the ÒClient versionÓ:

http://wormbasemanager.sourceforge.net/downloads/WBConverter__Client__Sources.tar.gz

and extract it on your computer.

To run the program, you must have Python; either install it manually [see section V.A of the Guide] or all the dependencies from the Debian Package ÒDependencies.debÓ.

Launch the ÒConfiguration wizardÓ and set up the programme as above.

 

3. Installing WormBase Converter Client on a Mac computer

If you never use ÒTerminalÓ on your Mac, you are probably much better off trying to find a PC to install the programme on; it will be much easier!

Otherwise, it is relatively simple. First download the ÒSourcesÓ for the ÒClient versionÓ:

http://wormbasemanager.sourceforge.net/downloads/WBConverter__Client__Sources.tar.gz

and extract it into the Applications folder on your computer.

You should see these files and directories:

If the .py files donÕt appear with a coloured icon, go to Python.org and download and install a recent version. You will also need to get the correct version of tcltk.

Once youÕve got the good version of Python running, launch the ÒConfiguration wizardÓ, and set up the programme as above. A terminal window also opens, but you can just ignore this! If IDLE is installed, this may be the default application for .py files. If so, you will need to change the preferred application to ÒPython LauncherÓ.

There, it wasnÕt too painful. Now you can run the application (WormBase Converter.py, using Python Launcher, not IDLE).

 

Further notes if running on a Mac

Due to the vagaries of computers, lists of genes copied and pasted from Excel that work perfectly well when running the PC client, can appear as a single line (single entry) on the Mac version. A simple work-around is to paste your list into TextEdit and under the ÒformatÓ menu, click on ÒMake plain textÓ, then copy this list into Wormbase Converter. Also the ÒReleaseÓ box may be empty. Clicking and de-clicking the ÒOnly data freezesÓ box solves the problem.

When youÕve done all this it will work; hereÕs the proof: