def _gatk4_cmd(jvm_opts, params, data): """Retrieve unified command for GATK4, using 'gatk'. GATK3 is 'gatk3'. """ gatk_cmd = utils.which(os.path.join(os.path.dirname(os.path.realpath(sys.executable)), "gatk")) return "%s && export PATH=%s:\"$PATH\" && gatk --java-options '%s' %s" % \ (utils.clear_java_home(), utils.get_java_binpath(gatk_cmd), " ".join(jvm_opts), " ".join([str(x) for x in params]))
def run(self, subcmd, opts, memscale=None): jvm_opts = get_picard_opts(self._config, memscale=memscale) cmd = ["export", "PATH=%s:$PATH" % utils.get_java_binpath(), "&&"] + \ [self._cmd] + jvm_opts + [subcmd] + ["%s=%s" % (x, y) for x, y in opts] + \ ["VALIDATION_STRINGENCY=SILENT"] do.run(utils.clear_java_home() + " && " + " ".join(cmd), "Picard: %s" % subcmd)
def gatk_cmd(name, jvm_opts, params, config=None): """Retrieve PATH to gatk using locally installed java. """ if name == "gatk": if isinstance(config, dict) and "config" not in config: data = {"config": config} else: data = config if not data or "gatk4" not in dd.get_tools_off(data): return _gatk4_cmd(jvm_opts, params, data) gatk_cmd = utils.which( os.path.join(os.path.dirname(os.path.realpath(sys.executable)), name)) # if we can't find via the local executable, fallback to being in the path if not gatk_cmd: gatk_cmd = utils.which(name) if gatk_cmd: return "%s && export PATH=%s:$PATH && %s %s %s" % \ (utils.clear_java_home(), utils.get_java_binpath(gatk_cmd), gatk_cmd, " ".join(jvm_opts), " ".join([str(x) for x in params]))
def gatk_cmd(name, jvm_opts, params, config=None): """Retrieve PATH to gatk using locally installed java. """ if name == "gatk": if isinstance(config, dict) and "config" not in config: data = {"config": config} else: data = config if not data or "gatk4" not in dd.get_tools_off(data): return _gatk4_cmd(jvm_opts, params, data) else: name = "gatk3" gatk_cmd = utils.which(os.path.join(os.path.dirname(os.path.realpath(sys.executable)), name)) # if we can't find via the local executable, fallback to being in the path if not gatk_cmd: gatk_cmd = utils.which(name) if gatk_cmd: return "%s && export PATH=%s:\"$PATH\" && %s %s %s" % \ (utils.clear_java_home(), utils.get_java_binpath(gatk_cmd), gatk_cmd, " ".join(jvm_opts), " ".join([str(x) for x in params]))
def run(self, subcmd, opts, memscale=None): jvm_opts = get_picard_opts(self._config, memscale=memscale) cmd = ["export", "PATH=%s:\"$PATH\"" % utils.get_java_binpath(), "&&"] + \ [self._cmd] + jvm_opts + [subcmd] + ["%s=%s" % (x, y) for x, y in opts] + \ ["VALIDATION_STRINGENCY=SILENT"] do.run(utils.clear_java_home() + " && " + " ".join(cmd), "Picard: %s" % subcmd)