Samuel's Tech Blog

Time for a little more "overview" like status update of the Bioclipse HPC Client part of the FIMS Project I'm working on for UPPNEX at UPPMAX.

Right now I'm hacking away on the batch job config wizard (just fixed a "select remote file" dialog, for file path parameters, which I actually even screencasted :=)).

Otherwise, I start coming to the stage when I need to do a decision about command line tool wrapper formats.

So far I've tried to use the Galaxy (bioinformatics portal) XML format, hoping to take advantage of the vast number of already wrapped bioinformatics tools (Actually, I'm using the format now - that is what drives the wizard in the Bioclipsescreencast above).

Unfortunately though, I figured out that most (if not all?) tool configs in Galaxy do not wrap the command line tool itself, but rather an accompanying script file (python/bash/perl), that does some additional stuff (different for each tool), which makes it hard to use the tool configs right away outside the galaxy platform.

So, realizing this, I'm considering whether we should go for something even more general, for this light-weight batch config wizard (which is not trying to be a complete replacement for Galaxy).

I actually just got to know about another such format (via a question on stack overflow). Apparently the docbook-package contains such a format! So, in case one would find that there are lots of ready-made such docbook-definitions for a bunch of cli tools already, then this could be quite interesting. ... so that's something I'll check in now. Otherwise, I maybe might as well stick with the Galaxy format (Have to admit though that the docbook one feels like a more general choice, in the general sense ... or what do you think?).

Then one could of course also have converters between the DocBook and Galaxy xml formats too ... should be pretty straight-forward with XSLT.

Ok, so that's where I am, and what I'm thinking about right now! Feel free to drop a line of feedback!