Exemple #1
0
    # TODO
    doblocks = 1
    if doblocks:

        sigproc_job_dict = {}
        basecaller_job_dict = {}
        alignment_job_dict = {}
        merge_job_dict = {}

        result_dirs = {}
        for block in blocks:
            result_dirs[block["id_str"]] = blockprocessing.initBlockReport(
                block,
                env["SIGPROC_RESULTS"],
                env["BASECALLER_RESULTS"],
                env["ALIGNMENT_RESULTS"],
                pluginbasefolder,
                env["oninstranalysis"],
            )

        # create a list of blocks
        blocks_to_process = []
        blocks_to_process.extend(blocks)
        timeout = 3 * 60 * 60
        if env["oninstranalysis"] and is_blockprocessing:
            timeout = 20 * 60 * 60

        env["block_dirs"] = [
            os.path.join(env["report_root_dir"], result_dirs[block["id_str"]]) for block in blocks_to_process
        ]
Exemple #2
0
    # dirs = ['%s/block_%s' % (SIGPROC_RESULTS, block['id_str']) for block in blocks]

    #####################################################
    # Create block reports                              #
    #####################################################

    #TODO
    doblocks = 1
    if doblocks:

        block_job_dict = {}
        merge_job_dict = {}

        result_dirs = {}
        for block in blocks:
            result_dirs[block['id_str']] = blockprocessing.initBlockReport(block, env['SIGPROC_RESULTS'], env['BASECALLER_RESULTS'], env['ALIGNMENT_RESULTS'], pluginbasefolder, from_sigproc_analysis=(env['blockArgs'] == "fromRaw"))


        # create a list of blocks
        blocks_to_process = []
        blocks_to_process.extend(blocks)
        timeout = 3*60*60
        if is_composite:
            if doSigproc:
                timeout =  1* 1*60 # sec , skip OIA, process diagnosis blocks
            else:
                timeout = 20*60*60 # sec

        plugins_params['block_dirs'] = [os.path.join(env['report_root_dir'],result_dirs[block['id_str']]) for block in blocks_to_process]

        while len(blocks_to_process) > 0 and timeout > 0:
Exemple #3
0
    #####################################################
    # Create block reports                              #
    #####################################################

    #TODO
    doblocks = 1
    if doblocks:

        sigproc_job_dict = {}
        basecaller_job_dict = {}
        alignment_job_dict = {}
        merge_job_dict = {}

        result_dirs = {}
        for block in blocks:
            result_dirs[block['id_str']] = blockprocessing.initBlockReport(block, env['SIGPROC_RESULTS'], env['BASECALLER_RESULTS'], env['ALIGNMENT_RESULTS'], pluginbasefolder, env['oninstranalysis'])

        # create a list of blocks
        blocks_to_process = []
        blocks_to_process.extend(blocks)
        timeout = 3*60*60
        if env['oninstranalysis'] and is_blockprocessing:
            timeout = 20*60*60

        env['block_dirs'] = [os.path.join(env['report_root_dir'],result_dirs[block['id_str']]) for block in blocks_to_process]

        while len(blocks_to_process) > 0 and timeout > 0:

            printtime('waiting for %s block(s) to schedule' % str(len(blocks_to_process)))
            sys.stdout.flush()
            sys.stderr.flush()
Exemple #4
0
    # Create block reports                              #
    #####################################################

    #TODO
    doblocks = 1
    if doblocks:

        sigproc_job_dict = {}
        basecaller_job_dict = {}
        alignment_job_dict = {}
        merge_job_dict = {}

        result_dirs = {}
        for block in blocks:
            result_dirs[block['id_str']] = blockprocessing.initBlockReport(
                block, env['SIGPROC_RESULTS'], env['BASECALLER_RESULTS'],
                env['ALIGNMENT_RESULTS'], pluginbasefolder,
                env['oninstranalysis'])

        # create a list of blocks
        blocks_to_process = []
        blocks_to_process.extend(blocks)
        timeout = 3 * 60 * 60
        if env['oninstranalysis'] and is_blockprocessing:
            timeout = 36 * 60 * 60

        env['block_dirs'] = [
            os.path.join(env['report_root_dir'], result_dirs[block['id_str']])
            for block in blocks_to_process
        ]

        while len(blocks_to_process) > 0 and timeout > 0: