ForEachFile#

Add to module run order:
#BioModule biolockj.module.diy.ForEachFile

Description#

Like GenMod, but done for each file in a previous module's output dir.

Properties#

Properties are the name=value pairs in the configuration file.

ForEachFile properties:#

Property Description
genMod.codeLine string
A line of code to create a one-line script. This is mutually exclusive with genMod.scriptPath. This is the preferred option for particularly simple scripts. This code will be executed using whatever system is specified by genMod.launcher.
default: null
genMod.launcher string
Define executable language command if it is not included in your $PATH
default: null
genMod.param string
parameters to pass to the user's script
default: null
genMod.resources list of file paths
path to one or more files to be copied to the module resource folder.
default: null
genMod.scriptPath file path
path to user script
default: null

General properties applicable to this module:#

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

Details#

version: 1.0.0 This is an extention of the GenMod module.
The given script is run for each file in the previous modules output dir. If there is no previous module, then the input files are used.The user script is run using a command:
[launcher] <script> <file path> [params]

Adds modules#

pre-requisite modules
none found
post-requisite modules
none found

Docker#

If running in docker, this module will run in a docker container from this image:

biolockjdevteam/blj_basic:v1.3.18

This can be modified using the following properties:
ForEachFile.imageOwner
ForEachFile.imageName
ForEachFile.imageTag

Citation#

Module developed by Ivory Blakley