Commit 3482754f authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Made codeMemory readable from outside

parent c1f9f9e8
...@@ -44,7 +44,8 @@ trait BiopetCommandLineFunction extends CommandLineFunction with Configurable { ...@@ -44,7 +44,8 @@ trait BiopetCommandLineFunction extends CommandLineFunction with Configurable {
var residentFactor: Double = config("resident_factor", default = 1.2) var residentFactor: Double = config("resident_factor", default = 1.2)
private var coreMemory: Double = _ private var _coreMemory: Double = 2.0
def coreMemeory = _coreMemory
var executable: String = _ var executable: String = _
...@@ -66,15 +67,15 @@ trait BiopetCommandLineFunction extends CommandLineFunction with Configurable { ...@@ -66,15 +67,15 @@ trait BiopetCommandLineFunction extends CommandLineFunction with Configurable {
if (threads == 0) threads = getThreads(defaultThreads) if (threads == 0) threads = getThreads(defaultThreads)
if (threads > 1) nCoresRequest = Option(threads) if (threads > 1) nCoresRequest = Option(threads)
coreMemory = config("core_memory", default = defaultCoreMemory).asDouble + (0.5 * retry) _coreMemory = config("core_memory", default = defaultCoreMemory).asDouble + (0.5 * retry)
if (config.contains("memory_limit")) memoryLimit = config("memory_limit") if (config.contains("memory_limit")) memoryLimit = config("memory_limit")
else memoryLimit = Some(coreMemory * threads) else memoryLimit = Some(_coreMemory * threads)
if (config.contains("resident_limit")) residentLimit = config("resident_limit") if (config.contains("resident_limit")) residentLimit = config("resident_limit")
else residentLimit = Some((coreMemory + (0.5 * retry)) * residentFactor) else residentLimit = Some((_coreMemory + (0.5 * retry)) * residentFactor)
if (!config.contains("vmem")) vmem = Some((coreMemory * (vmemFactor + (0.5 * retry))) + "G") if (!config.contains("vmem")) vmem = Some((_coreMemory * (vmemFactor + (0.5 * retry))) + "G")
if (vmem.isDefined) jobResourceRequests :+= "h_vmem=" + vmem.get if (vmem.isDefined) jobResourceRequests :+= "h_vmem=" + vmem.get
jobName = configName + ":" + (if (firstOutput != null) firstOutput.getName else jobOutputFile) jobName = configName + ":" + (if (firstOutput != null) firstOutput.getName else jobOutputFile)
......
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