Example #1
0
                           name = 'mcmc_',
                           mem = 3)

    #LAUNCH EYEBALL JOBS
    eyeball.launch()

    
    #RETURN A LIST OF LAUNCHED JOBS
    return dict(cmds=eyeball.cmds,
                inputs = inp_dicts)



def run_single(run_id):
    '''
Given an input dictionary containing a single paramater set
run mcmc in matlab using bs_macros.run_matlab.
'''
    input_dict = butils.load_data(run_id,'input')
    return bsm.runmat('run_mcmc', input_dict, run_id)


if __name__ == '__main__':
    run_id = sys.argv[2]
    run_func = globals()[sys.argv[1]]
    output_dict = run_func(run_id)
    if output_dict == None:
        output_dict = {'blank':'Nothing output in call to {0}'.\
                           format(sys.argv[1])}
    bsu.save_data( output_dict, run_id, 'output')
Example #2
0
            inp_dicts.append(dict(similarities=sims, self_similarity=percentile(sims.flatten(), p)))
    else:
        inp_dicts = butils.load_data(run_id, "input")

    eyeball = bsub.eyeball(
        run_id, os.path.abspath(inspect.stack()[0][1]), inp_dicts, func="test_bsubfun", name=run_id + "_test_", mem=2
    )

    eyeball.launch()
    eyeball.await()
    eyeball.package()
    eyeball.complete()


def usage():
    print """
usage: bsub_clusters function run_id

Call function with run_id.
"""
    exit(1)


if __name__ == "__main__":
    run_id = sys.argv[2]
    run_func = globals()[sys.argv[1]]
    output_dict = run_func(run_id)
    if output_dict == None:
        output_dict = {"blank": "Nothing output in call to {0}".format(sys.argv[1])}
    butils.save_data(output_dict, run_id, "output")
Example #3
0
In any event, the family name is stored in the
input dict so there will be no problems running the
script is the run_id does not conform to this format.
'''
    inp_dict = bsub.load_data(run_id, 'input')
    inp_run_id = inp_dict['inp_run_id']
    rfid = inp_dict['family']

    output = tutils.run(rfid, run_id, inp_run_id, reset=True)
    return output


def usage():
    print '''
usage: rna_ali2d function run_id

Call function with run_id.
'''
    exit(1)


if __name__ == '__main__':
    run_id = sys.argv[2]
    run_func = globals()[sys.argv[1]]
    output_dict = run_func(run_id)
    if output_dict == None:
        output_dict = {'blank':'Nothing output in call to {0}'.\
                           format(sys.argv[1])}
    bsu.save_data(output_dict, run_id, 'output')
Example #4
0
    eyeball = bsub.eyeball(run_id,
                           os.path.abspath(inspect.stack()[0][1]),
                           inp_dicts,
                           func='test_bsubfun',
                           name=run_id + '_test_',
                           mem=2)

    eyeball.launch()
    eyeball. await ()
    eyeball.package()
    eyeball.complete()


def usage():
    print '''
usage: bsub_clusters function run_id

Call function with run_id.
'''
    exit(1)


if __name__ == '__main__':
    run_id = sys.argv[2]
    run_func = globals()[sys.argv[1]]
    output_dict = run_func(run_id)
    if output_dict == None:
        output_dict = {'blank':'Nothing output in call to {0}'.\
                           format(sys.argv[1])}
    butils.save_data(output_dict, run_id, 'output')