runScript

The runScript command allows you to batch multiple projects of the same type (e.g. assembly, computeSNPs). There are required three file: 1) a runScript file with variables, 2) a file with a table of values for the variables, and 3) a script file specifying the action to be carried out.

Example (runScript file):

setDefaultDirectory directory: “.”
   set $force: false
   set $DataDisk: “/Volumes/Raid/DataDisk”
   set $ResultDisk: “/Volumes/ResultDisk”
   set $MergeDisk: “/Volumes/MergeDisk0”
   set $snp:true
   set $snpMethod:”Diploid”
   set $repCnt:100
   set $merLayoutMin:19
   diskPath path: {“${MergeDisk}/mergeSort Data”}}
   runScript table: “testAssembly.txt” script: “testAssembly.template.script”

Example (table file):

defaultDir template query isPair seqTech project merSize snp snpMethod
“${ResultDisk}/rice” ${DataDisk}/rice.genome ${DataDisk}/rice FALSE Illumina rice 21 TRUE Diploid
“${ResultDisk}/ecoli” ${DataDisk}/Ecoli.gbk ${DataDisk}/ecoli TRUE Illumina Ecoli 21 TRUE Diploid
“${ResultDisk}/Exome” ${DataDisk}/GRCh37.gbk ${DataDisk}/Sample1 FALSE 454 HuEx 19 TRUE Diploid

Example (script file):

; “assembly.template.script”
setMachineMemory memory:32
setDefaultDirectory directory: $defaultDir
compareSeqs template: $template
query: {file: $query
isPair: $isPair
seqTech: $seqTech}
directoryMer: “intermediateFiles”
; directoryQueryMer: “intermediateFiles”
hits: “intermediateFiles/${project}.hits”
layout: “intermediateFiles/${project}.layout”
output: “results_${mersize}_${merSkipQuery}/${project}”
; results per project results: “${project}.results.txt”
; aggregate all results
results: “${ResultDisk}/assembly.results.txt”
merSize: $mersize
merSkipQuery: $merSkipQuery
repeatCnt: $repCnt
merLayoutMin: $merLayoutMin
layoutType: once
maxGap: 6
format: BAM
onePackage: true
snp: $snp
snpMethod: $snpMethod
; snp_writeExtended: true
forceMake: $force

Parameters for this command are described below: