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 haven’t 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 “C:” drive, not just onto the desktop. There are very complete installation instructions in the file “Documentation.pdf” in the Help folder. But briefly, after downloading and extracting, launch the “Configuration Wizard”.

Description: config.tiff

Enter “http://www.ciml.univ-mrs.fr/applications/WB_converter” as the host address.

Then when you hit “Test the server”, it should look like this:

Then hit “SAVE THIS CONFIGURATION”.

That’s all! You can now launch the application.

2. Installing WormBase Converter Client on a linux computer

 

To install the software under Linux, download the “Sources” for the “Client version”:

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 “Dependencies.deb”.

Launch the “Configuration wizard” and set up the programme as above.

 

3. Installing WormBase Converter Client on a Mac computer

If you never use “Terminal” 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 “Sources” for the “Client version”:

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 don’t 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 you’ve got the good version of Python running, launch the “Configuration wizard”, 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 “Python Launcher”.

There, it wasn’t 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 “format” menu, click on “Make plain text”, then copy this list into Wormbase Converter. Also the “Release” box may be empty. Clicking and de-clicking the “Only data freezes” box solves the problem.

When you’ve done all this it will work; here’s the proof: