Welcome to ASGARD's on line docs
I am in setting it up, should be usable in a few days...
Code from CVS should be always more up-to-date than the packaged version. If you are having any problems with ASGARD, please check the CVS repository for the latest versions of the different programs. In due time, changes from those will become a new packaged version. Until then, one can simply replace the old scripts with the new ones.
Since July 1st, 2011, KEGG's FTP is only available through subscription. Therefore, the automated download of KEGG data in ASGARD no longer works. If you have a subscription, please manually download the required data (as per instructions from the download_ASGARD_data script). If you do not need KEGG data, then you can safely ignore this.