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Run shell script from windows batch file
  1. Copy files to unix server (seems you have this solved)

  2. Use plink program from putty package to start command in unix server. Needed is a ssh daemon running in unix server. Output of command in remote server can be obtained and readed to know file copy has ended.

  3. Generate the touch files. break > filename is sufficient to generate a file with 0 bytes.

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