BeeExperiment

BeeExperiment is a drastic rewrite of the original open project in an effort to explore new ideas, highlight possible changes, and act as an educational endeavor. Some of the goals undertaken were:

• Individually package and logically separate Bee-Launcher from Bee-Orchestrator.

• Construct and implement a new architecture to support targeting a variety of management systems while ensuring that the core functionality remains consistent.

• Propose a standardized algorithm in conjunction with a new class structure.s.

• Re-engineer BeeFlow while keeping the core concepts found intact.

• Greatly expand the structure of both the beefile in addition to beeflow file.

• Introduce structure for supporting Bee-Monitor and Bee-Logging through improved status tracking.

IMPORTANT This project features on going work, epically with regards to incorporating better documentation. In addition I have identified a few bugs and will going forward (due to the switch from private -> public repo) attempt to be more proactive about documenting these.

Deployment Instructions

Requirements

• Linux
• Bash
• Screen
• Charliecloud (recommended)
• Anaconda (recommended)

$ conda create -n bxp python=3.6 python
$ source activate bxp
$ git clone https://github.com/paulbry/beeexperiment
$ cd BeeExperiment/src
$ pip install . ---user
$ export PATH=$HOME/.local/bin:$PATH

From 0 to Experiment

1. Create the following hello.beefile, note that is assumes the use of a Anaconda environment name bxp (conda -n <name>)

   id: helloWorld
   label: Basic hello world example
   requirements:
       EnvVarRequirements:
         envDef:
           - PATH: $HOME/.local/bin
         sourceDef:
           - activate: bxp
   workerBees:
       - Task:
         - touch:
             flags:
               - randomFile.txt
   terminateAfter: true
   baseCommand: env

2. Verify source activate bxp.

3. bee-launcher -l hello.beffile will launch workflow in a screen

4. bee-orchestrator --orc -t hello will allow you to see the launch

Copyright

TODO

NOTES

This work is derived from BEE: Build and Executed

In addition attributes from the Common Workflow Language and Software Carpentry but is not nearly CWL compliment at this time.