switched to most recent version of STAR
Adapted python stub to the latest STAR SOP

- extended and reformatted arg-parser to give users better information
  on the available options
- added more possibilities to add read group information to the BAM
  header (@RG line) based on direct input or a tcga xml file.
- replaced downstream usage of samtools with alternatives that are part
  of STAR (sorting, multiple input fast files)
- allowed alignment of single end read sets
- added additional decompression setting for bzips
Extended Dockerfile

- added bzip
- added pip to install more python packages
- added lxml package
- corrected install of STAR from previous commit
Reworked read group logic

- read group information in header does now support multiple input files
- improved data management --> data can be written to tmp directory
- add junctions as output file for two pass run
- clean up data after STAR run
- cleaned code from old comment-lines
Merge branch 'master' of github.com:akahles/icgc_rnaseq_align
removed absolute path to STAR
Adapted code to comply with latest header specs

- add comment line to header
- add legacy sample ID
- fix wrong info in some of the fields
- minor code cleanup
Adapted upload specs for STAR

- adapted STAR version in xml template
- changed perl script to dynamically fill in run command into xml
Merge pull request #1 from akahles/master

Update to first version of STAR alignment SOP