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.
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: