scripts/support/mirnas/precompute.py
def launch_new_rfsearch(family_dir, cpu=4):
    """
    Launches a new LSF job

    family_dir: The location of a valid family directory
    cpus: Number of CPUs to use per thread

    return: void
    """

    lsf_err_file = os.path.join(family_dir, "auto_rfsearch.err")
    lsf_out_file = os.path.join(family_dir, "auto_rfsearch.out")

    job_name = os.path.basename(family_dir)

    cmd = ''
    if os.path.exists(os.path.join(family_dir, "DESC")) is False:
        # LSF command to be executed
        cmd = ("bsub -M %s -o %s -e %s -n %s -g %s -q production-rh74 "
               "-J %s \"cd %s && rfsearch.pl -t 25 -cnompi -q production-rh74 -relax -nodesc\"")
    else:
        cmd = ("bsub -M %s -o %s -e %s -n %s -g %s -q production-rh74 "
               "-J %s \"cd %s && rfsearch.pl -t 25 -cnompi -q production-rh74 -relax -ignoresm\"")
    
    file_extensions = ["cmsearch", "tbl", "err"]
    
    for file_type in file_extensions:
	
	subprocess.call("rm %s/*.%s" % (family_dir, file_type), shell=True)
	
    # call command
    #print (cmd % (MEMORY, lsf_out_file, lsf_err_file, cpu, LSF_GROUP, job_name, family_dir))
    subprocess.call(cmd % (MEMORY, lsf_out_file, lsf_err_file,
                          cpu, LSF_GROUP, job_name, family_dir), shell=True)

    Launches a new LSF job

    family_dir: The location of a valid family directory
    cpus: Number of CPUs to use per thread

    return: void
    
Launches a new LSF job
family_dir: The location of a valid family directory
cpus: Number of CPUs to use per thread

void
Launches a new LSF job family_dir : The location of a valid family directory cpus : Number of CPUs to use per thread void
def launch_new_rfsearch(family_dir, cpu=4):
    lsf_err_file = os.path.join(family_dir, "auto_rfsearch.err")
    lsf_out_file = os.path.join(family_dir, "auto_rfsearch.out")
    job_name = os.path.basename(family_dir)
    cmd = ''
    if os.path.exists(os.path.join(family_dir, "DESC")) is False:
        cmd = ("bsub -M %s -o %s -e %s -n %s -g %s -q production-rh74 "
               "-J %s \"cd %s && rfsearch.pl -t 25 -cnompi -q production-rh74 -relax -nodesc\"")
    else:
        cmd = ("bsub -M %s -o %s -e %s -n %s -g %s -q production-rh74 "
               "-J %s \"cd %s && rfsearch.pl -t 25 -cnompi -q production-rh74 -relax -ignoresm\"")
    file_extensions = ["cmsearch", "tbl", "err"]
    for file_type in file_extensions:
	subprocess.call("rm %s/*.%s" % (family_dir, file_type), shell=True)
    subprocess.call(cmd % (MEMORY, lsf_out_file, lsf_err_file,
                          cpu, LSF_GROUP, job_name, family_dir), shell=True)
def launch_new_rfsearch ( family_dir , cpu = 4 ) : lsf_err_file = os . path . join ( family_dir , "auto_rfsearch.err" ) lsf_out_file = os . path . join ( family_dir , "auto_rfsearch.out" ) job_name = os . path . basename ( family_dir ) cmd = '' if os . path . exists ( os . path . join ( family_dir , "DESC" ) ) is False : cmd = ( "bsub -M %s -o %s -e %s -n %s -g %s -q production-rh74 " "-J %s \"cd %s && rfsearch.pl -t 25 -cnompi -q production-rh74 -relax -nodesc\"" ) else : cmd = ( "bsub -M %s -o %s -e %s -n %s -g %s -q production-rh74 " "-J %s \"cd %s && rfsearch.pl -t 25 -cnompi -q production-rh74 -relax -ignoresm\"" ) file_extensions = [ "cmsearch" , "tbl" , "err" ] for file_type in file_extensions : subprocess . call ( "rm %s/*.%s" % ( family_dir , file_type ) , shell = True ) subprocess . call ( cmd % ( MEMORY , lsf_out_file , lsf_err_file , cpu , LSF_GROUP , job_name , family_dir ) , shell = True )
Launches a new LSF job
family_dir: The location of a valid family directory
cpus: Number of CPUs to use per thread
Launches a new LSF job family_dir : The location of a valid family directory cpus : Number of CPUs to use per thread
"""
    Launches a new LSF job

    family_dir: The location of a valid family directory
    cpus: Number of CPUs to use per thread

    return: void
    """ # LSF command to be executed # call command #print (cmd % (MEMORY, lsf_out_file, lsf_err_file, cpu, LSF_GROUP, job_name, family_dir))
family_dir
cpu