changes to tophat
Merge branch 'homer_chipseq'
convert relative path of configs to absolutes ones
smokebox changes (e.g. header)
merge with upsteam (allpower)
Code beautifications
support for job recovery

first batch of mods converted
first version of smokebox and bowtie2 independance
merge with upsteam fork

merging testframework
remove accidentally submitted file
remove accidentally submitted merge files
support for job recovery

second batch of pipelines refactored to allow job recovery
recovering mode enabled in more mods

also old scripts removed
code beautified
bugfixes
Bugfixes
Bugfixes
delete tmp files
changes
logfile notes
merge with fork