comparison gistic.xml @ 2:da03207b002d draft default tip

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1:d16928a77255

    <exit_code range=":-1" />
  </stdio>

  <command>
    <![CDATA[
      ##export included matlab paths. This was done in dependencies but seems to need reseting periodically 

      export LD_LIBRARY_PATH=\$GISTIC_DIR/MATLAB_Component_Runtime/v714/runtime/glnxa64:\$GISTIC_DIR/MATLAB_Component_Runtime/v714/sys/os/glnxa64:\$GISTIC_DIR/MATLAB_Component_Runtime/v714/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:\$GISTIC_DIR/MATLAB_Component_Runtime/v714/sys/java/jre/glnxa64/jre/lib/amd64/server:\$GISTIC_DIR/MATLAB_Component_Runtime/v714/sys/java/jre/glnxa64/jre/lib/amd64;

      export XAPPLRESDIR=\$GISTIC_DIR/MATLAB_Component_Runtime/v714/X11/app-defaults;

      ##make directory for results
      mkdir ./results;
      touch ./results/sig_regions.bed; 
      ##start command line
      \$GISTIC_DIR/gp_gistic2_from_seg 

2:da03207b002d

    <exit_code range=":-1" />
  </stdio>

  <command>
    <![CDATA[
      ##make directory for results
      mkdir ./results;
      touch ./results/sig_regions.bed; 
      ##start command line
      \$GISTIC_DIR/gp_gistic2_from_seg