Add file demultiplex_multiple_index_runs
demultiplex_multiple_index_runs.py script to run demultiplexing with
indexes of different length
more changes to demultiplex_multiple_index_runs
	- added option to keep original index (needed for molecular tagging)
	- added function for fastq_utils to return number of bases with quality
>Q30
	- output almost all the information needed to mimic
Demultiplex_stats.htm
fastq_utils.py now uses streams in place of files in order to read and
wirte in a more efficent way

Fix problems in reported statistics

This is a working version
Added funcitonality to demultiplex only specified indexes:
 -it overwrites existing Unmultiplexed and Ambiguous folders
Handeling Miseq runs
Handeling Miseq runs
updated statusdb connection for setting up pipeline config files
sending user survey
added survey module
read and update lims udf
gene names missing in fpkm_table.txt. Fixed in correl.R.
remoove printing
Launch pipeline using pm module
merge conflicts
Merge pull request #336 from senthil10/master

Launch pipeline using pm module
Merge pull request #335 from mayabrandi/master

RNA-seq pipe update
to load udfs into the reference database
change of adaprorsize 121 to 136
merge conflicts