greatlse/workflows

Kepler workflows created by NBCR

Contents

• Workflow documentation requirements
• Workflow distribution requirements
• File "listing.rst"
• Adding a new workflow

Workflow documentation requirements

1. Required files

   For hosting the workflow on NBCR website each workflow must have the following files:

   • workflow PNG image
   • workflow kar file
   • text file description which contains a describing of the workflow. Please see a section below describing the file format and an example templates/description-workflow file.
   • README file with any additional information about the workflow. If there are any extra files intended for download with the workflow they must be listed in README.
   • input/ directory with example input files
   • output/ directory with example output for the example input input files
   • Optional: any extra files (documentation, notes, etc.) that will be distributed with the workflow. Must be listed in README.

2. File "templates/description-workflow" format

   This file consists of a description of a worflow as key-value pairs. Keywords are ordered one per line followed by keyword values. Values can have multiple lines. The following keywords are required:

   • Name workflow name in upper camel case. No dashed or spaces.
   • Version workflow version
   • Class actor or workflow
   • Kar kar file name
   • Image image file name
   • Tag a list of tags separated by spaces. A tag can be a software namew used in the workflow (for example, Amber) or a generic description of some part of the workflow (for example: trajectory, minimization, etc.)
   • Type of a workflow. Valid values are Clustering, Docking, Electrostatic, MDsimulation, Utilities. More values will be added when more workflows are created.
   • Director a kepler director. Valid values: DDF, DDP, PN, SDF. Can be only one director.
   • Actor list of actors used in the workflow (names separated by spaces). Default value is None
   • Description short description of what this workflow does.
   • Required software description of the prerequisite software. Can be 1 or more lines, one software item per line. If no software is required the value is none.
   • Parameters description of worflow parameters, one parameter per paragraph. Each description starts with a parameter short name followed by the explanation text of wht this parameter does. Note text alignment.
   • Overview any addition information about the workflow specifics. Default value is None
   • Usage a short description of how to use the workflow

   See an example templates/description-workflow file.

3. Versioning convention

   Each workflow must have a unique version number which is a sequence-based identifier in the form of major.minor[.revision]:

   • major number is increased when there are significant jumps in functionality
   • minor number is incremented when only minor features or significant fixes have been added
   • revision number is incremented when minor bugs are fixed.

4. Naming convention

   Each workflow name includes a text written as upper CamelCase followed by a _ and a version. For example: LigandSimulation_1.2.3.

5. Example

   The workflow for ligand simulation will have the following files:

   • LigandSimulation_1.2.3.kar
   • LigandSimulation_1.2.3.png
   • description
   • README
   • input/
   • output/
   • LigandSimulation_1.2.3.notes (optional file)

Workflow distribution requirements

Workflows are distributed as tar.gz files which must contain :

• workflow kar file
• README file
• any optional files (extra documentation or examples)

Naming convention: WorkflowName_1.2.tar.gz

File "listing.rst"

This file keeps track of the names for workflows, actors, types and tags. Please consult this file when creating new workflows and update accordingly when creating new workflows.

Adding a new workflow

• create a directory either in workflows/ or actors/
• in the listing.rst:
  • add workflow name
  • add new tags or types (if any)