Merge pull request #1 from severinb/master

The latest stable version from the webserver
deleted the old Template and COMPONENT folders
changes in the repeatMask file
change in GetSequences component
the fmitools has been re-added!
the RunPhylogibbs component is changed to autmatically perform WM trimming.
the RunPhylogibbs component is changed to autmatically perform WM trimming.
changes in RepeatsOut and RunMotevo, and plus adding a new component which is called FitBackgroundPriorAndBeta. This new component fits the prior background and the beta over the test_pool sequences. Note that the sequences must be single species -- no alignment, and in the MotEvo parameter file we are setting background frequency to uniform -- 0.25 for each nucleotide. There is no use of UFE as well.
fixings in RepeatsOut component
fixings bugs in RepeatsOut and also the cProfiler is added to a few components, some bugs in RunPhyloggibs is resolved
fixings bugs in Phyloggibs component
Adding the Refined Motif component to the component library
Resolving an error in MotifRefinement component
The FitBackgroundPriorAndBeta component is added to the component set
Component CalculateEnrichmentScore is added
Component FitBackgroundPriorAndBeta is changed for the YAML output
Fixed a bug in YAML writing in component FitBackgroundPriorAndBeta
Component CalculateEnrichmetScore is added
the network file is being changed by adding the MotifRefinement, FittingBetaPrior parameters and EnrichmentScore to the current pipeline
The modified weblogo-3.4 is added to the scripts. In addition a minor changes is being made in MotifRefinement component to use the modified weblogo in order to generate the motifs.