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HPCI-0.75
River stage one • 3 direct dependents • 3 total dependents
/ HPCI::Subgroup

NAME

    HPCI::Subgroup

SYNOPSIS

Treat a collection of stages and/or subgroups like a single stage.

DESCRIPTION

A subgroup is a collection of stages and/or subgroups. It acts both as a group and as a stage:

  1. It acts as a stage to the group or subgroup that contains it, except that it is created using the parent group or subgroup's subgroup method instead of the stage method. The child subgroup's name can be provided to the parent group or subgroup's add_deps method to specify order dependency between the subgroup (i.e. all of its component stages and/or subgroups treated as a single unit) and other components of the parent.

  2. It acts as a group to the stages and/or subgroups that it contains. For example, it has stage, subgroup, and add_deps methods.

There are a number of purposes to using a subgroup.

  1. The subgroup can be used for assigning a dependency. A prerequisite to a subgroup must complete before any of the components of the subgroup can commence; a dependent to a subgroup cannot commence until all of the components of the subgroup have completed.

  2. The subgroup can list file requirements that apply to the collection. That can define the attributes of files used in multiple stages; can specify in files that must be present before the subgroup can start; specify skip conditions that will cause the entire subgroup to be skipped; specify out, delete, or rename files to be verified or processed when the subgroup has completed.

  3. Allow different stages to use the "same" name. The name must still be different from the names of all stages (and subgroups) that can be dependency targets. That includes its parent (sub)group and all of its other top level components, its grandparent (sub)group and all of its top level components, and similarily for great**n grandparent groups and all of their top level components. So, it cannot have to same name as a sibling, (great)*parent, or (great)*uncle, but it can have the same name as cousins and more distantly connected components.

    The full name used for a stage or subgroup is actually composed like a pathname, using the group and parent subgroups and the final component name all separated by slashes. (e.g. GROUP/SUBGROUP/STAGE)

When a subgroup is specified as a dependency, none of its component stages or subgroups execute until prerequisite components have completed; and all of its component stages and subgroups must have finished before any dependent component will be allowed to execute.

A subgroup is creating using the subgroup method of either a group or subgroup object.

ATTRIBUTES

The attributes for this class are pulled in from HPCI::Super and HPCI::Sub. Super contains all the characteristics common to container classes (Group and Subgroup), while Sub contains all the characteristics common to contained classes (Subgroup and Stage).

AUTHOR

Christopher Lalansingh - Boutros Lab

John Macdonald - Boutros Lab

ACKNOWLEDGEMENTS

Paul Boutros, Phd, PI - Boutros http://www.omgubuntu.co.uk/2016/03/vineyard-wine-configuration-tool-linuxLab

The Ontario Institute for Cancer Research