Friday, January 14, 2011

I just thought I should show you...

Hm that title is not quite true actually. It was more along the roads of egonw++ asked me to blog about Bioclipse headless. He told me that I should be friendly to potential early adapters. I told him there isn't really much to blog about yet. Which got him asking: "It compiles, no?", at which point I decided to give up. I did put up some more fighting just for the looks of it but he had me. So what exactly is this all about then?

I have been working on the headless branch lately (actually branches because a lot of our repos now have headless branches). The idea is to make the bioclipse scripting environment know as BSL accesible from the command line. The first step has been to refactor away all gui dependencies from the core bioclipse plugins and I am far from finished with that yet. I have played a little with a command line loop for interactively coding and what exists today is just the JavaScript loop made accessible from the command line. It fires up a lot of Bioclipse stuff in the background and my hopes is that the publication of the very first Bioclipse manager into it is within reach but to all of you early adopters out there (yea my best guess it that means you Egon (but anyone else reading, feel free to prove me wrong) :) the only thing you can expect to see if you manage to get the thing running is just a JavaScript prompt looking something like this:


  1. Jonathan, thanx for blogging this! It's nice to get a glimpse of the future, and being able to run BSL scripts without a full GUI is important, and will mean that people can explore science on their desktop and later repeat their work periodically (e.g. using a crontab), or remotely on a HPC cluster, etc, etc.

    So, how do people get this code running on their machine? Can it be build without a GUI too, using Buckminster?

  2. yea, that is something that has to be looked into. I want to set up a job on our Hudson builder which actually builds a downloadable version of the bsl-runner complete with all currently working managers.