major changes to PATHMARK under development
small bug fix
added new test case and shazam-cytoscapeweb
need fix for absolute path for non-galaxy runs
added cytoscapeweb files
update to galaxy pipelining
updates to galaxy test
wasn't passing pathway file
added circlePlot.py
merging a few changes from this branch to another
fixed a feature sorting bug in signature
added Rscript version of limma
update to example
updated example to match new code
update to galaxy code
galaxy bug fix
galaxy bug fix
added options for new permute methods
minor syntax fix
using absolute paths in make