* Running
  
  perl ~/../GROUP/Pipeline2/Scripts/pipeline.pl pipeline.conf &> pipeline.log &
  
  Usually working directory contains two files "pipeline.conf" and "regions",
  options for pipeline and regions of interest respectively.
  
  Examples could be found here:
  [[file:~pachko/hg19_13.12.2011/][working directory example]]

* Conf file
  example: [[file:example_pipeline.conf][example pipeline.conf]]
  If "ALIGN_METHOD" option is set to "none" pipeline stops after extracting sequences.
  
  If "MOTEVOC_PARAMS" option is set to "none" pipeline stops after aligning sequences.
  
  Individual alignment files by default are in dir "ALIGNMENT" (option
  "ALIGN_OUT_DIR"). Concatenated alignments ready for motevo processing are
  in file "final_out.aln".

* Regions file
  Regions file contains coordinates for regions of interest. Configuration
  option "REGIONS_FILE".
  
  example:
  chr1	68590	69590	+	hg19_v1_chr1_+_69090_69090
  chr1	367139	368158	+	hg19_v1_chr1_+_367639_367658
  chr1	762487	763540	+	hg19_v1_chr1_+_762987_763040

  Values are tab separated.
  first column -- chromosome
  second column -- start position
  third column -- end position
  fourth column -- strand
  fifth column -- optional, could contain any information. In the example this is promoter id 
