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All Samples(21)  |  Call(21)  |  Derive(0)  |  Import(0)

src/a/r/ARC-HEAD/ARC/runners/assembler.py   ARC(Download)
            args += ['-cdna']
        args += [os.path.join(self.params['target_dir'], 'assembly')]
        logger.debug("Calling newAssembly for sample: %s target %s" % (sample, target))
        logger.info(" ".join(args))
        ret = subprocess.call(args, stdout=out, stderr=out)
        #Build args for addRun:
        if 'assembly_PE1' in self.params and 'assembly_PE2' in self.params:
            args = ['addRun', os.path.join(self.params['target_dir'], 'assembly')]
            args += [self.params['assembly_PE1']]
            logger.debug("Calling addRun for sample: %s target %s" % (sample, target))
            args += [self.params['assembly_PE1']]
            logger.debug("Calling addRun for sample: %s target %s" % (sample, target))
            logger.debug(" ".join(args))
            ret = subprocess.call(args, stdout=out, stderr=out)
 
            args = ['addRun', os.path.join(self.params['target_dir'], 'assembly')]
            args += [self.params['assembly_PE2']]
            logger.debug("Calling addRun for sample: %s target %s" % (sample, target))
            logger.debug(" ".join(args))

src/a/r/ARC-HEAD/ARC/runners/base.py   ARC(Download)
    def debug(self, msg):
        if self.loglevel == logging.DEBUG:
            name = self.name
            logger.debug("%-12s| %s" % (name, msg))
 

src/a/r/ARC-HEAD/ARC/spawn.py   ARC(Download)
    def run(self):
        logger.info("Starting...")
        logger.debug("Setting up workers.")
 
        for i in range(self.nprocs):
                # This shouldn't be needed but we will check just in case
                if self.all_workers_waiting():
                    logger.debug("Workers are all waiting and the queue is empty.  Exiting")
                    break
                else:
                    logger.debug("Workers are not in a waiting state.  Waiting for more.")
    def killall(self):
        for i in range(self.nprocs):
            logger.debug("Shutting down %s" % (self.workers[i].name))
            self.workers[i].terminate()
            self.workers[i].join()
 
    def all_workers_waiting(self):
        waiting = 0
        for i in range(self.nprocs):
            logger.debug("ProcessRunner %d reports %d" % (i, self.status[i]))

src/a/r/ARC-HEAD/ARC/process_runner.py   ARC(Download)
        self.running()
        job = getattr(ARC.runners, item['runner'])(item['params'])
        logger.debug("[%s] Processing: %s" % (self.name, job.message()))
        job.queue(self.q)
        job.runner()
                os.kill(self.ppid, signal.SIGINT)
            except (KeyboardInterrupt, SystemExit):
                logger.debug("Process interrupted")
            except Exception as e:
                ex_type, ex, tb = sys.exc_info()

src/a/r/ARC-HEAD/ARC/runners/mapper.py   ARC(Download)
 
        logger.info("Sample: %s Calling blat mapper" % self.params['sample'])
        logger.debug(" ".join(args))
        try:
            ret = subprocess.call(args, stdout=out, stderr=out)

src/a/r/ARC-HEAD/ARC/runners/assembly_checker.py   ARC(Download)
            # params = deepcopy(self.params)
            # finisher = Finisher(params)
            logger.debug("Sample: %s, iteration %s, Submitting finisher job to queue." % (sample, self.params['iteration']))
            self.submit(Finisher.to_job(params))
            logger.info("Sample: %s Assemblies finished: %s of %s targets completed" % (sample, completed, len(self.params['targets'])))