Editing BioMicroCenter:IlluminaDataPipeline (section)

== Executing the Pipeline ==

=== Parameter File ===
The parameter file contains information about the pipeline for GERALD. This is an example file:

  12345678:ANALYSIS eland_extended
  12345678:ELAND_SEED_LENGTH 25
  123:ELAND_GENOME /data/Genome/Eland/RefGenome_Eland_sacCersgd
  5:ELAND_GENOME /data/Genome/Eland/RefGenome_Eland_PhiX
  4678:ELAND_GENOME /data/Genome/Eland/RefGenome_Eland_mm9
  USE_BASES Y*n
  ELAND_MULTIPLE_INSTANCES 4

ANALYSIS TYPES = eland_extended (>32nt), eland_paired, eland_tag, sequence (no alignment), or none (failed lanes only) <br>
* "eland" is no longer supported in 1.3.2, so keep 1.0 around if you want to keep iterative ELAND.

USE_BASE = Y*n is the standard, using every base except the last but is mutable. For example, if you must omit the first two bases, you could insert nnY*n instead.
* Multiplex: Using multiplex can be done with the I tag. For example Y*nI6n would take all bases upto the final 8 with the middle 6 being used as the index.

ELAND_MULTIPLE_INSTANCES can only be 1,2,4,8. Using any other value will default to 1.

=== Pipeline Execution ===
The following commands will execute the pipeline on the BMC servers.
   
  $ cd /mnt/bmc-store/current/run<1-4>/<DATE_HWI->/
  $ /data/apps/pkg/GAPipeline/GAPipeline-1.0/Goat/goat_pipeline.py --GERALD=<parameter file> --control-lane=<phiX> Images/ or IPARR/
       or 
  $ /data/apps/pkg/GAPipeline/GAPipeline-1.3.2/bin/goat_pipeline.py --GERALD=<parameter file> --control-lane=<phiX> Images/ 
       or 
  $ /data/apps/pkg/GAPipeline/GAPipeline-1.3.2/bin/bustard.py --GERALD=<parameter file> --control-lane=<phiX> Data/IPAR_1.3/

Use "--control-lane=" to select a lane <n> that is to be used to estimate phasing and matrix correction for all other lanes. Control lanes are necessary for samples with skewed base compositions.


if you execute without errors, proced to make the pipeline
  $ /data/apps/pkg/GAPipeline/GAPipeline-1.0/Goat/goat_pipeline.py --GERALD=<parameter file> --control-lane=<phiX> --make Images/ or IPARR/
       or 
  $ /data/apps/pkg/GAPipeline/GAPipeline-1.3.2/bin/goat_pipeline.py --GERALD=<parameter file> --control-lane=<phiX> --make Images/ 
       or 
  $ /data/apps/pkg/GAPipeline/GAPipeline-1.3.2/bin/bustard.py --GERALD=<parameter file> --control-lane=<phiX> Data/IPAR_1.3/


Move to the Firecrest Directory (for 1.0) or Bustard directory (for 1.3.2):
  $ cd Data/C1-36_Firecrest....
          or
  $ cd Data/IPAR_1.3/Bustard...
          then
  $ make recursive -j8 >& <DATE>_Analysis.log &

.

[[BioMicroCenter:DataArchiving]]