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biopet.biopet
Commits
88edfd84
Commit
88edfd84
authored
Oct 27, 2016
by
Sander Bollen
Browse files
Merge branch 'feature-walltime' into 'develop'
Fix for BIOPET-399 See merge request !466
parents
18dd271e
a0cd735e
Changes
2
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biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala
View file @
88edfd84
...
...
@@ -40,16 +40,22 @@ trait CommandLineResources extends CommandLineFunction with Configurable {
def
defaultResidentFactor
:
Double
=
1.2
var
vmemFactor
:
Double
=
config
(
"vmem_factor"
,
default
=
defaultVmemFactor
)
val
useSge
:
Boolean
=
config
(
"use_sge"
,
default
=
true
)
var
residentFactor
:
Double
=
config
(
"resident_factor"
,
default
=
defaultResidentFactor
)
private
var
_coreMemory
:
Double
=
2.0
def
coreMemory
=
_coreMemory
/** This value is for SGE and is defined in seconds */
protected
val
maxWalltimeLimit
:
Option
[
Int
]
=
config
(
"max_walltime_limit"
)
var
retry
=
0
override
def
freezeFieldValues
()
:
Unit
=
{
setResources
()
if
(
vmem
.
isDefined
)
jobResourceRequests
:+=
"h_vmem="
+
vmem
.
get
if
(
useSge
&&
vmem
.
isDefined
)
jobResourceRequests
:+=
s
"h_vmem=${vmem.get}"
if
(
useSge
&&
maxWalltimeLimit
.
isDefined
)
jobResourceRequests
:+=
s
"h_rt=${maxWalltimeLimit.get}"
super
.
freezeFieldValues
()
}
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
View file @
88edfd84
...
...
@@ -16,11 +16,10 @@ package nl.lumc.sasc.biopet.core
import
java.io.File
import
htsjdk.samtools.SAMSequenceDictionary
import
htsjdk.samtools.reference.
{
FastaSequenceFile
,
IndexedFastaSequenceFile
}
import
htsjdk.samtools.reference.IndexedFastaSequenceFile
import
nl.lumc.sasc.biopet.core.summary.
{
Summarizable
,
SummaryQScript
}
import
nl.lumc.sasc.biopet.utils.
{
BamUtils
,
ConfigUtils
,
FastaUtils
,
Logging
}
import
nl.lumc.sasc.biopet.utils.
config.
{
Config
,
Configurable
}
import
nl.lumc.sasc.biopet.utils.
config.
{
Config
,
Configurable
}
import
nl.lumc.sasc.biopet.utils.
{
Config
Utils
,
FastaUtils
,
Logging
}
import
scala.collection.JavaConversions._
...
...
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