code: def upgrade_thirdparty_tools(args, remotes):
      
      cbl = get_cloudbiolinux(remotes)
      if args.toolconf and os.path.exists(args.toolconf):
          package_yaml = args.toolconf
      else:
          package_yaml = os.path.join(cbl["dir"], "contrib", "flavor",
                                      "ngs_pipeline_minimal", "packages-conda.yaml")
      sys.path.insert(0, cbl["dir"])
      cbl_conda = __import__("cloudbio.package.conda", fromlist=["conda"])
      cbl_conda.install_in(_get_conda_bin(), args.tooldir, package_yaml)
      manifest_dir = os.path.join(_get_data_dir(), "manifest")
      print("Creating manifest of installed packages in %s" % manifest_dir)
      cbl_manifest = __import__("cloudbio.manifest", fromlist=["manifest"])
      if os.path.exists(manifest_dir):
          for fname in os.listdir(manifest_dir):
              if not fname.startswith("toolplus"):
                  os.remove(os.path.join(manifest_dir, fname))
      cbl_manifest.create(manifest_dir, args.tooldir)
docs: Install and update third party tools used in the pipeline.
  
      Creates a manifest directory with installed programs on the system.