installation instructions cgatools:


reference data
------------------------
   Get .crr files from CG ftp site:
      - ftp://ftp.completegenomics.com/ReferenceFiles/build36.crr
      - ftp://ftp.completegenomics.com/ReferenceFiles/build37.crr
  
   Get calibration root file:
      - ftp://ftp.completegenomics.com/ScoreCalibrationFiles/var-calibration-v2.tgz

   Get other reference file from CG ftp site:
      - ftp://ftp.completegenomics.com/AnnotationFiles/gene36.tsv.gz
      - ftp://ftp.completegenomics.com/AnnotationFiles/rmsk36.tsv.gz
      - ftp://ftp.completegenomics.com/AnnotationFiles/segdup36.tsv.gz
      - ftp://ftp.completegenomics.com/AnnotationFiles/gene37.tsv.gz
      - ftp://ftp.completegenomics.com/AnnotationFiles/rmsk37.tsv.gz
      - ftp://ftp.completegenomics.com/AnnotationFiles/segdup37.tsv.gz


   And unzip them to desired location.


   Adjust cgatools.loc file (included in repository) to reflect the locations of the reference files you dowloaded.


datatypes
------------------------

 <!-- Start Complete Genomics Datatypes -->
    <datatype extension="cg_var" type="galaxy.datatypes.completegenomics:CG_Var" display_in_upload="true" />
    <datatype extension="cg_mastervar" type="galaxy.datatypes.completegenomics:CG_MasterVar" display_in_upload="true" />
    <datatype extension="cg_gene" type="galaxy.datatypes.completegenomics:CG_Gene" display_in_upload="true" />
 <!-- End Complete Genomics Datatypes -->