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#BioModule com.github.fodorlab.envVar.ShowShepVar
This module gets the value of the environment variable "SHEP" and prints its value to the log and an output file. The variable must be set in the environment using the local system or the -e parameter to BioLockJ.
Properties are the name=value pairs in the configuration file.
none
| Property | Description |
|---|---|
| cluster.batchCommand | string Terminal command used to submit jobs on the cluster default: null |
| cluster.jobHeader | string Header written at top of worker scripts default: null |
| cluster.modules | list List of cluster modules to load at start of worker scripts default: null |
| cluster.prologue | string To run at the start of every script after loading cluster modules (if any) default: null |
| cluster.statusCommand | string Terminal command used to check the status of jobs on the cluster default: null |
| docker.saveContainerOnExit | boolean If Y, docker run command will NOT include the --rm flag default: null |
| docker.verifyImage | boolean In check dependencies, run a test to verify the docker image. default: null |
| script.defaultHeader | string Store default script header for MAIN script and locally run WORKER scripts. default: #!/bin/bash |
| script.numThreads | integer Used to reserve cluster resources and passed to any external application call that accepts a numThreads parameter. default: 8 |
| script.numWorkers | integer Set number of samples to process per script (if parallel processing) default: 1 |
| script.permissions | string Used as chmod permission parameter (ex: 774) default: 770 |
| script.timeout | integer Sets # of minutes before worker scripts times out. default: null |
version: 0.0.0 none
pre-requisite modules
none found
post-requisite modules
none found
If running in docker, this module will run in a docker container from this image:
biolockjdevteam/biolockj_controller:v1.4.1
This can be modified using the following properties:
ShowShepVar.imageOwner
ShowShepVar.imageName
ShowShepVar.imageTag
BioModule created by Ivory Blakley as part of the test suite for BioLockJ.