Has anyone used maqgene?

I need analysis some deep sequencing data. I know maqgene is the best one to assemble C. elegans deep sequence data, but it runs in Linux system which I have never used before.

I followed the instructions published on Nature Methods 6, 549 (2009), but I don’t know how to set up URL to download exon annotation. Can anyone help me out.

I installed ubuntu 10.04