March 3, 2017

Installing PlasMapper

Yesterday I found a strange thing - a piece of open-source bioinformatics software that only needed minor tweaking before it would run. Top marks to the authors, although they might like to read the following to learn how they can make it absolutely perfect!

The software in question is PlasMapper. It Just Works (TM) if you follow the installation steps, EXCEPT you need to bear in mind the following points:

  1. Follow the instructions to the end, except don't run ant install yet.
  2. In build.xml locate and edit the servletjar property to remove common from the path - this makes it work with Sun's JDK. (Ignore the comments about not editing below a certain point).
  3. Edit src/ca/ualberta/xdong/plasMapper/annotate/plasMapConfiguration_en_CA.properties and globally change /home/tomcat to match your Tomcat home directory, just as you were instructed to do so in build.xml.
  4. Now run ant install as per the instructions.
  5. If you want to be completely strict, you need to either copy the PlasMapper tgz file into the webapps/PlasMapper folder inside Tomcat, or edit the index page to remove the 'download source' link.

That's it though. Relatively painless compared to some projects out there!

PS. If you were having trouble getting the prerequisites right, on Ubuntu it works simply by typing:

apt-get install sun-java6-jdk tomcat6

Topics: Bioinformatics, Bioinformatics, installing, Open source, PlasMapper, problems