Installing Tioga on Leopard

Written by thomas on April 4th, 2008

Since I do DNA analysis in Ruby, I wanted to be able to make some nice graphs for my data. Enter Tioga, a Ruby library originally created by "Bill Paxton, one of the creators of Adobe PostScript". Needless to say, the graphs look beautiful.

Anyway, I wasn't able to install it on Leopard. Installing via gem didn't produce a workable Tioga, so I had to do it the old fashioned way:

tar zxf tioga-1.7.tar.gz
cd tioga-1.7
cd split
ruby extconf.rb

Now, the last command failed with this error message:

checking for zlib.h... no
Error: you should have zlib (including development files) installed to
build and run Tioga. You can get it there:

  http://www.zlib.net/

If that doesn't solve your problem, please report it on the Tioga tracker:

  http://rubyforge.org/tracker/?group_id=701

After a lot of debugging, the problem was solved by instead running the following:

hdrdir="/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/universal-darwin9.0" \
ARCHFLAGS="-arch i386" ruby extconf.rb

Mind you, this is on a Mac Pro, which should otherwise have ARCHFLAGS="-arch x86_64". Moving on, running the rest of the code is a piece of cake.

make
sudo make install
cd ../tests
ruby ts_Tioga.rb

Ta-da! It should work, and you can start working with Tioga. Enjoy!

New design

Written by thomas on November 21st, 2006

Hurray! My brand, spanking, shining new design is up and running. Hopefully, there won’t be too many bugs. Let me tell you, working around the heap of bugs that constitute the web browser called Internet Explorer, is not fun. In any case, the theme should look decent from IE 6 and up. IE 5.0 is just too broken to bother with, and no sane person should be running that anyway. I’ve tested the design in Opera 9, Firefox 2, Safari 2, ELinks 0.9.2, IE 5, IE 5.5, IE 6, and IE 7.

If you see something that looks like a theme bug, please let me know! Maybe I’ll release this theme some day, if people really want it, but for now, it feels good having a theme that nobody else has. ;-)

In dealing with my new theme, i found that I had to modify the LaTeX plugin somewhat. Here is the updated patch.

Mephisto LaTeX plugin patch

Written by thomas on November 7th, 2006

After a reinstall of Mephisto everything’s back up and running as it should. Now, back on topic.

When researching the available blogging softwares, I ran across Mephisto in an attempt of finding myself a Ruby on Rails based software. One of my primary wishes for my new blog was the ability to easily include [LaTeX] equations in my webpages. The only viable alternative which had LaTeX support was WordPress, which I’ve been told has quite a number of issues. After some inquiring in the #mephisto channel, somebody offered to code up a plugin, and a couple of days later the LatexRenderer plugin was born.

Excellent as it was, I still wanted more ;) A couple of versions later, the LatexRenderer patch was done. The original plugin takes the code as:

< filter : latex >
$x = \frac{-b\pm\sqrt{b^2 - 4ac}}{2a}$
< / filter : latex >

, minus the spaces that is, and renders the equation as an image.

What I added to the plugin was the ability to quickly show the underlying LaTeX source code. Rendering the above equation now gives us:

If you click on the equation, the image disappears and the source code appears. Click again, and you’ll get the image back.

I hope somebody will find this a useful feature, and hopefully Jan will include the patch in the official plugin.