- [web] move CASSIS to a dedicated web server
- [web] update MEME to version 4.12.0 (web version still used v4.9.0)
- [web] add academic title for Thomas Wolf and Neetika Nath
- Workaround for bug in MEME's XML output, introduced in MEME v4.11.x
- Add support for FIMO v4.11.4 and newer
- Add citing information to readme
- [web] move source code, binaries and changelog to github
- [web] attach promoter positions file to results email
- [web] remove absolute paths from log file
- [web] properly remove old files from results dir
- small adjustment to copyright text
- add check if (adjusted) promoter set still has at least 4 sequences if (original) set exceeded upstream cluster border
- [web] add a more clear phrase to the result email, if no cluster was predicted and no error occurred
- [web] always attach log file to result email
- fix problem with different input line seperators in files created on Linux vs. files created on Windows machines
- fix small typo in upstream cluster extension code (if gap length == 5)
- [web] improve handling of filenames without extensions
- [web] job submission summary: add error message if anchor gene does not occur in annotation file
- fix bug in promoter sequence calculation
- improve error messages
- fix bug which causes false reports of faulty promoters in cluster predictions
- improve some regular expressions to avoid problems with meta-characters in gene names
- drop support for AspGD, JGI, GFF, … annotation file formats (caused quite some trouble)
- introduce self-defined annotation file format
- [web] improve handling of unusual file names
- CASSIS is now able to work with MEME suite versions newer than v4.9.1 (preserving backwards compatibility with older versions, like v4.9.1)
- improve handling of tainted $PATH variables
- provide SiTaR as an alternative to MEME/FIMO, if TFBSs are already known and don't need to be predicted de novo
- better error handling
- small improvements