scripts/export/genomes/genome_fetch.py
def lsf_cmd_generator(upid, gca_acc, domain, exec_path, proj_dir):
    """
    Generates an lsf job command for downloading a new genome. Returns an
    LSF specific bsub command

    upid: Uniprot's reference proteome id
    gca_acc: ENA's genome accession. -1 if there's no available id
    domain: Proteome's taxonomic domain
    exec_path: The path to the pipeline executable
    proj_dir: The path to the project directory
    """

    subdir_idx = upid[8:]
    prot_dir = os.path.join(os.path.join(proj_dir, subdir_idx), upid)

    cmd = ("bsub -M %s "
           "-R \"rusage[mem=%s,tmp=%s]\" "
           "-o \"%s\" "
           "-e \"%s\" "
           "-u \"%s\" "
           "-n 4 "
           "-Ep \"rm -rf luigi\" "
           "-g %s "
           "python %s DownloadGenome --upid %s --gca-acc %s --project-dir %s --domain %s") % (
               gc.MEM, gc.MEM, gc.TMP_MEM,
               os.path.join(prot_dir, "download.out"),
               os.path.join(prot_dir, "download.err"),
               gc.USER_EMAIL, gc.LSF_GEN_GROUP,
               exec_path, upid, gca_acc,
               proj_dir, domain)

    return cmd

    Generates an lsf job command for downloading a new genome. Returns an
    LSF specific bsub command

    upid: Uniprot's reference proteome id
    gca_acc: ENA's genome accession. -1 if there's no available id
    domain: Proteome's taxonomic domain
    exec_path: The path to the pipeline executable
    proj_dir: The path to the project directory
    
Generates an lsf job command for downloading a new genome. Returns an
LSF specific bsub command

Uniprot's reference proteome id
gca_acc: ENA's genome accession. -1 if there's no available id
domain: Proteome's taxonomic domain
exec_path: The path to the pipeline executable
proj_dir: The path to the project directory
Generates an lsf job command for downloading a new genome . Returns an LSF specific bsub command Uniprot ' s reference proteome id gca_acc : ENA ' s genome accession . - 1 if there ' s no available id domain : Proteome ' s taxonomic domain exec_path : The path to the pipeline executable proj_dir : The path to the project directory
def lsf_cmd_generator(upid, gca_acc, domain, exec_path, proj_dir):
    subdir_idx = upid[8:]
    prot_dir = os.path.join(os.path.join(proj_dir, subdir_idx), upid)
    cmd = ("bsub -M %s "
           "-R \"rusage[mem=%s,tmp=%s]\" "
           "-o \"%s\" "
           "-e \"%s\" "
           "-u \"%s\" "
           "-n 4 "
           "-Ep \"rm -rf luigi\" "
           "-g %s "
           "python %s DownloadGenome --upid %s --gca-acc %s --project-dir %s --domain %s") % (
               gc.MEM, gc.MEM, gc.TMP_MEM,
               os.path.join(prot_dir, "download.out"),
               os.path.join(prot_dir, "download.err"),
               gc.USER_EMAIL, gc.LSF_GEN_GROUP,
               exec_path, upid, gca_acc,
               proj_dir, domain)
    return cmd
def lsf_cmd_generator ( upid , gca_acc , domain , exec_path , proj_dir ) : subdir_idx = upid [ 8 : ] prot_dir = os . path . join ( os . path . join ( proj_dir , subdir_idx ) , upid ) cmd = ( "bsub -M %s " "-R \"rusage[mem=%s,tmp=%s]\" " "-o \"%s\" " "-e \"%s\" " "-u \"%s\" " "-n 4 " "-Ep \"rm -rf luigi\" " "-g %s " "python %s DownloadGenome --upid %s --gca-acc %s --project-dir %s --domain %s" ) % ( gc . MEM , gc . MEM , gc . TMP_MEM , os . path . join ( prot_dir , "download.out" ) , os . path . join ( prot_dir , "download.err" ) , gc . USER_EMAIL , gc . LSF_GEN_GROUP , exec_path , upid , gca_acc , proj_dir , domain ) return cmd
Generates an lsf job command for downloading a new genome.
Generates an lsf job command for downloading a new genome .
"""
    Generates an lsf job command for downloading a new genome. Returns an
    LSF specific bsub command

    upid: Uniprot's reference proteome id
    gca_acc: ENA's genome accession. -1 if there's no available id
    domain: Proteome's taxonomic domain
    exec_path: The path to the pipeline executable
    proj_dir: The path to the project directory
    """
upid
gca_acc
domain
exec_path
proj_dir