Genome indexing management tools added
Fix a bug in case of several transcripts or genes having identical
location.
Aligner index management tools added
Genome lists synchronized for BWA. Bowtie, Bowtie2 and Tophat2
Merge branch 'master' of https://github.com/chipster/chipster.git
Genome indexing tools updated.
Reimplemented the update functionality in bundle.py

diff_bundle() should now support several files with same checksum
Latest genome updates to install scripts
Merge branch 'master' of https://github.com/chipster/chipster.git
Version to 2.6.2
Several fixes to bundle.py and to_bundle.py

- added function annotations
- fixed tuple being passed to refine_path()
- changed copy_file() to always use shutil.copy2()
- cleaned up detect_move() and subfunction old_new()
- changed default installation path to /opt/chipster
Merge remote-tracking branch 'upstream/master'