How to use _create_run_command method in localstack

Best Python code snippet using localstack_python

cluster.py

Source:cluster.py

...62        # FIXME: this is not a good place to run install, and it only works because we're63        #  assuming that there will only ever be one running Elasticsearch cluster64        install.install_elasticsearch(self.version)65        self._init_directories()66        cmd = self._create_run_command(additional_settings=self.command_settings)67        cmd = " ".join(cmd)68        user = constants.OS_USER_ELASTICSEARCH69        if is_root() and user:70            # run the elasticsearch process as a non-root user (when running in docker)71            cmd = f"su {user} -c '{cmd}'"72        env_vars = self._create_env_vars()73        LOG.info("starting elasticsearch: %s with env %s", cmd, env_vars)74        t = ShellCommandThread(75            cmd,76            env_vars=env_vars,77            strip_color=True,78            log_listener=self._log_listener,79        )80        t.start()81        return t82    def _log_listener(self, line, **_kwargs):83        LOG.info(line.rstrip())84    def _create_run_command(85        self, additional_settings: Optional[CommandSettings] = None86    ) -> List[str]:87        # delete Elasticsearch data that may be cached locally from a previous test run88        dirs = self.directories89        bin_path = os.path.join(dirs.base, "bin/elasticsearch")90        # build command settings for bin/elasticsearch91        settings = {92            "http.port": self.port,93            "http.publish_port": self.port,94            "transport.port": "0",95            "network.host": self.host,96            "http.compression": "false",97            "path.data": f'"{dirs.data}"',98            "path.repo": f'"{dirs.backup}"',...

_mutect2_variantcaller.py

Source:_mutect2_variantcaller.py

...5from .._pipeline_config import PipelineConfig6from ._variantcallers import _Callable, _VariantCaller7class Mutect2VariantCaller(_Callable, _VariantCaller):8    @classmethod9    def _create_run_command(10        cls, caller_config: PipelineConfig, library_paths: LibraryPaths11    ) -> list:12        bam_paths = cls._get_bam_paths(caller_config)13        germline_sample_name = cls._get_sample_name(bam_paths["germline_bam_path"])14        tumor_sample_name = cls._get_sample_name(bam_paths["tumor_bam_path"])15        output_name = cls._create_output_filename(16            caller_config, sample_name=tumor_sample_name17        )18        command = [19            library_paths.GATK4,20            "Mutect2",21            "-R",22            library_paths.REF_DIR,23            "-I",24            bam_paths["tumor_bam_path"],25            "-tumor",26            tumor_sample_name,27            "-I",28            bam_paths["germline_bam_path"],29            "-normal",30            germline_sample_name,31            "-O",32            output_name,33        ]34        return command35    @classmethod36    def _create_get_snp_variants_command(37        cls, caller_config: Dict, library_paths: LibraryPaths38    ) -> str:39        bam_paths = cls._get_bam_paths(caller_config)40        tumor_sample_name = cls._get_sample_name(bam_paths["tumor_bam_path"])41        input_name = cls._create_output_filename(42            caller_config, sample_name=tumor_sample_name43        )44        output_name = cls._create_output_filename(45            caller_config, sample_name=f"SNP_{tumor_sample_name}"46        )47        command = [48            library_paths.GATK4,49            "SelectVariants",50            "-R",51            library_paths.REF_DIR,52            "-V",53            input_name,54            "--select-type-to-include",55            "SNP",56            "-O",57            output_name,58        ]59        return command60    @classmethod61    def _create_get_indel_variants_command(62        cls, caller_config: Dict, library_paths: LibraryPaths63    ) -> str:64        bam_paths = cls._get_bam_paths(caller_config)65        tumor_sample_name = cls._get_sample_name(bam_paths["tumor_bam_path"])66        input_name = cls._create_output_filename(67            caller_config, sample_name=tumor_sample_name68        )69        output_name = cls._create_output_filename(70            caller_config, sample_name=f"SNP_{tumor_sample_name}"71        )72        command = [73            library_paths.GATK4,74            "SeleckVariants",75            "-R",76            library_paths.REF_DIR,77            "-V",78            input_name,79            "--select-type-to-include",80            "INDEL",81            "-O",82            output_name,83        ]84        return command85    @classmethod86    def _create_get_other_variants_command(87        cls, caller_config: Dict, library_paths: LibraryPaths88    ) -> str:89        bam_paths = cls._get_bam_paths(caller_config)90        tumor_sample_name = cls._get_sample_name(bam_paths["tumor_bam_path"])91        input_name = cls._create_output_filename(92            caller_config, sample_name=tumor_sample_name93        )94        output_name = cls._create_output_filename(95            caller_config, sample_name=f"SNP_{tumor_sample_name}"96        )97        command = [98            library_paths.GATK4,99            "SeleckVariants",100            "-R",101            library_paths.REF_DIR,102            "-V",103            input_name,104            "--select-type-to-exclude",105            "SNP",106            "--select-type-to-exclude",107            "INDEL",108            "-O",109            output_name,110        ]111        return command112    @classmethod113    def call_variants(cls, caller_config: Dict):114        library_paths = LibraryPaths()115        mutect_command = cls._create_run_command(116            caller_config=caller_config, library_paths=library_paths117        )118        get_snp_command = cls._create_get_snp_variants_command(119            caller_config=caller_config, library_paths=library_paths120        )121        get_indel_command = cls._create_get_indel_variants_command(122            caller_config=caller_config, library_paths=library_paths123        )124        get_other_variants_command = cls._create_get_other_variants_command(125            caller_config=caller_config, library_paths=library_paths126        )127        run(mutect_command, cwd=caller_config.VCF_OUTPUT_DIR)128        run(get_snp_command, cwd=caller_config.VCF_OUTPUT_DIR)129        run(get_indel_command, cwd=caller_config.VCF_OUTPUT_DIR)...

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