zenotech / MyCluster

           depends_on_always_run=False):

    job_id = None

    if depends_on and depends_on_always_run:

        cmd = 'bsub -w "ended(%s)" < %s ' % (depends_on, script_name)

        with os.popen(cmd) as f:

            output = f.readline()

            try:

                job_id = int(output.split(' ')[1].replace(

                    '<', '').replace('>', ''))

            except:

                print 'Job submission failed: ' + output

    elif depends_on is not None:

        cmd = 'bsub -w "done(%s)" < %s ' % (depends_on, script_name)

        with os.popen(cmd) as f:

            output = f.readline()

            try:

                job_id = int(output.split(' ')[1].replace(

                    '<', '').replace('>', ''))

            except:

                print 'Job submission failed: ' + output

    else:

        with os.popen('bsub <' + script_name) as f:

            output = f.readline()

            try:

                job_id = int(output.split(' ')[1].replace(

                    '<', '').replace('>', ''))

            except:

                print 'Job submission failed: ' + output

    return job_id

           depends_on_always_run=False):

    job_id = None

    if not immediate:

        if depends_on and depends_on_always_run:

            with os.popen('sbatch --kill-on-invalid-dep=yes --dependency=afterany:%s %s' % (depends_on, script_name)) as f:

                output = f.readline()

                try:

                    job_id = int(output.split(' ')[-1].strip())

                except:

                    print 'Job submission failed: ' + output

        elif depends_on is not None:

            with os.popen('sbatch --kill-on-invalid-dep=yes --dependency=afterok:%s %s' % (depends_on, script_name)) as f:

                output = f.readline()

                try:

                    job_id = int(output.split(' ')[-1].strip())

                except:

                    print 'Job submission failed: ' + output

        else:

            with os.popen('sbatch ' + script_name) as f:

                output = f.readline()

                try:

                    job_id = int(output.split(' ')[-1].strip())

                except:

                    print 'Job submission failed: ' + output

                # Get job id and record in database

    else:

        with os.popen('grep -- "SBATCH -p" ' + script_name + ' | sed \'s/#SBATCH//\'') as f:

def submit(script_name, immediate, depends_on=None,

           depends_on_always_run=False):

    job_id = None

    if not immediate:

        if depends_on and depends_on_always_run:

            with os.popen('qsub -W depend=afterany:%s %s' % (depends_on, script_name)) as f:

                output = f.readline()

                try:

                    job_id = output.strip().split('.')[0]

                except:

                    print 'Job submission failed: ' + output

        elif depends_on is not None:

            with os.popen('qsub -W depend=afterok:%s %s' % (depends_on, script_name)) as f:

                output = f.readline()

                try:

                    job_id = output.strip().split('.')[0]

                except:

                    print 'Job submission failed: ' + output

        else:

            with os.popen('qsub ' + script_name) as f:

                output = f.readline()

                try:

                    job_id = output.strip().split('.')[0]

                except:

                    print 'Job submission failed: ' + output

    else:

        print "immediate not yet implemented for PBS"

    return job_id