github.com/informationsea/shellflow@v0.1.3/docs/source/configuration.rst (about)

     1  Configuration
     2  =============
     3  
     4  Shellflow can be configured GridEngine options or other options with
     5  TOML file.
     6  
     7  Command
     8  -------
     9  
    10  RegExp
    11  ~~~~~~
    12  
    13  If a command to run is matched to a regular expression, options listed
    14  in below will be applied.
    15  
    16  RunImmediate
    17  ~~~~~~~~~~~~
    18  
    19  If this option is setted to true, command will be run immediately
    20  without using job scheduler.
    21  
    22  DontInheirtPath
    23  ~~~~~~~~~~~~~~~
    24  
    25  If this option is setted to true, Shellflow will not inheirt ``PATH``
    26  and ``LD_LIBRARY_PATH`` when running with job scheduler.
    27  
    28  SGEOption
    29  ~~~~~~~~~
    30  
    31  This options will be passed to Univa/Sun Grid Engine ``qsub``.
    32  
    33  Configuration Example
    34  ---------------------
    35  
    36  .. code:: toml
    37  
    38      [[Command]]
    39      RegExp = "mkdir +(-p +)?[^;&]+"
    40      RunImmediate = true
    41  
    42      [[Command]]
    43      RegExp = "example_dont_inheirt_path"
    44      DontInheirtPath = true
    45  
    46      [[Command]]
    47      RegExp = "gatk .*"
    48      SGEOption = ["-l", "s_vmem=20G,mem_req=20G", "-pe", "def_slot", "2"]
    49  
    50      [[Command]]
    51      RegExp = "samtools .*"
    52      SGEOption = ["-l", "s_vmem=10G,mem_req=10G", "-pe", "def_slot", "2"]
    53  
    54      [[Command]]
    55      RegExp = "java .*"
    56      SGEOption = ["-l", "s_vmem=40G,mem_req=40G"]