run_gbs_qc

#!/bin/sh

function get_pipeline() {
   export SEQ_PRISMS_BIN=/dataset/gseq_processing/active/bin/gbs_prism/seq_prisms
   export GBS_PRISM_BIN=/dataset/gseq_processing/active/bin/gbs_prism
   cd $GBS_PRISM_BIN
   gbs_version=$1

   # (to move to another KGD version, git pull  in the KGD folder, and then check out the version you want)
   kgd_version=`$GBS_PRISM_BIN/get_kgd_version.sh`
   echo "preparing to run gbs qc pipeline version $gbs_version (KGD version $kgd_version) (press enter to continue)"
   read answer
   is_alpha=`echo $gbs_version | grep alpha`
   if [ ! $is_alpha ]; then 
      git checkout -q $gbs_version 
      if [ $? != 0 ]; then
         echo "unable to checkout pipeline version $gbs_version"
         exit 1
      fi
      exec ./_run_gbs_qc -i $gbs_version $kgd_version
   else
      echo "(no checkout for alpha versions, just running in current branch)"
      exec ./_run_gbs_qc -i $gbs_version $kgd_version
   fi
}

get_pipeline 1.0.4alpha