code: def run_genesippr(self):
          
          from pathlib import Path
          home = str(Path.home())
          logging.info('GeneSippr')
          # These unfortunate hard coded paths appear to be necessary
          miniconda_path = os.path.join(home, 'miniconda3')
          miniconda_path = miniconda_path if os.path.isdir(miniconda_path) else os.path.join(home, 'miniconda')
          logging.debug(miniconda_path)
          activate = 'source {mp}/bin/activate {mp}/envs/sipprverse'.format(mp=miniconda_path)
          sippr_path = '{mp}/envs/sipprverse/bin/sippr.py'.format(mp=miniconda_path)
          for sample in self.metadata:
              logging.info(sample.name)
  
              # Run the pipeline. Check to make sure that the serosippr report, which is created last doesn't exist
              if not os.path.isfile(os.path.join(sample.genesippr_dir, 'reports', 'genesippr.csv')):
                  cmd = 'python {py_path} -o {outpath} -s {seqpath} -r {refpath} -F'\
                      .format(py_path=sippr_path,
                              outpath=sample.genesippr_dir,
                              seqpath=sample.genesippr_dir,
                              refpath=self.referencefilepath
                              )
                  logging.critical(cmd)
                  # Create another shell script to execute within the PlasmidExtractor conda environment
                  template = "#!/bin/bash\n{activate} && {cmd}".format(activate=activate,
                                                                       cmd=cmd)
                  genesippr_script = os.path.join(sample.genesippr_dir, 'run_genesippr.sh')
                  with open(genesippr_script, 'w+') as file:
                      file.write(template)
                  # Modify the permissions of the script to allow it to be run on the node
                  self.make_executable(genesippr_script)
                  # Run shell script
                  os.system('/bin/bash {}'.format(genesippr_script))
docs: Run GeneSippr on each of the samples