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biopet.biopet
Commits
9f2940e0
Commit
9f2940e0
authored
Mar 20, 2015
by
Peter van 't Hof
Browse files
Change limits to coreMemory
parent
1ff52e09
Changes
38
Hide whitespace changes
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
View file @
9f2940e0
...
...
@@ -44,7 +44,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
override
val
versionExitcode
=
List
(
0
,
1
)
override
def
versionCommand
=
executable
+
" --version"
override
val
default
Vmem
=
"6G"
override
val
default
CoreMemory
=
4.0
override
val
defaultThreads
=
8
var
sam
:
Boolean
=
config
(
"sam"
,
default
=
true
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
View file @
9f2940e0
...
...
@@ -33,7 +33,7 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
override
val
defaultThreads
=
8
/** default vmem for cluster jobs */
override
val
default
Vmem
=
"8G"
override
val
default
CoreMemory
=
6.0
/** input file */
@Input
(
doc
=
"Input file (SAM or BAM)"
,
required
=
true
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
View file @
9f2940e0
...
...
@@ -35,7 +35,7 @@ class Gsnap(val root: Configurable) extends BiopetCommandLineFunction {
override
val
defaultThreads
=
8
/** default vmem for cluster jobs */
override
val
default
Vmem
=
"16G"
override
val
default
CoreMemory
=
10.0
/** input file */
@Input
(
doc
=
"Input FASTQ file(s)"
,
required
=
true
)
//var input: List[File] = _
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
View file @
9f2940e0
...
...
@@ -33,7 +33,7 @@ class Pbzip2(val root: Configurable) extends BiopetCommandLineFunction {
var
decomrpess
=
true
var
memory
:
Option
[
Int
]
=
config
(
"memory"
)
override
val
default
Vmem
=
(
memory
.
getOrElse
(
1000
)
*
2
/
1000
)
+
"G"
override
val
default
CoreMemory
=
memory
.
getOrElse
(
1000
)
.
toDouble
/
1000
override
val
defaultThreads
=
2
override
def
beforeCmd
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
View file @
9f2940e0
...
...
@@ -36,7 +36,7 @@ trait RscriptCommandLineFunction extends BiopetCommandLineFunction {
protected
var
script
:
File
=
_
protected
var
scriptName
:
String
=
_
protected
var
arguments
:
ListBuffer
[
String
]
=
ListBuffer
()
override
val
default
Vmem
:
String
=
"4G"
override
val
default
CoreMemory
=
2.0
executable
=
config
(
"exe"
,
default
=
"Rscript"
,
submodule
=
"R"
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
View file @
9f2940e0
...
...
@@ -64,7 +64,7 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction {
override
val
versionExitcode
=
List
(
0
,
1
)
/// Stampy uses approx factor 1.1 times the size of the genome in memory.
override
val
default
Vmem
=
"4G"
override
val
default
CoreMemory
=
4.0
override
val
defaultThreads
=
8
override
def
versionCommand
=
executable
+
" --help"
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
View file @
9f2940e0
...
...
@@ -63,7 +63,7 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
var
outFileNamePrefix
:
String
=
_
var
runThreadN
:
Option
[
Int
]
=
config
(
"runThreadN"
)
override
val
default
Vmem
=
"6G"
override
val
default
CoreMemory
=
4.0
override
val
defaultThreads
=
8
/** Sets output files for the graph */
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
View file @
9f2940e0
...
...
@@ -32,7 +32,7 @@ class Tophat(val root: Configurable) extends BiopetCommandLineFunction {
override
val
versionExitcode
=
List
(
0
,
1
)
override
def
versionCommand
=
executable
+
" --version"
override
val
default
Vmem
=
"6G"
override
val
default
CoreMemory
=
4.0
override
val
defaultThreads
=
8
@Input
(
doc
=
"FastQ file(s) R1"
,
shortName
=
"R1"
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
View file @
9f2940e0
...
...
@@ -46,7 +46,7 @@ class BedtoolsCoverage(val root: Configurable) extends Bedtools {
if
(
input
.
getName
.
endsWith
(
".bam"
))
inputTag
=
"-abam"
}
override
val
default
Vmem
=
"6G"
override
val
default
CoreMemory
=
4.0
/** Returns command to execute */
def
cmdLine
=
required
(
executable
)
+
required
(
"coverage"
)
+
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
View file @
9f2940e0
...
...
@@ -60,7 +60,7 @@ class BwaAln(val root: Configurable) extends Bwa {
var
n2
:
Boolean
=
config
(
"2"
,
default
=
false
)
var
Y
:
Boolean
=
config
(
"Y"
,
default
=
false
)
override
val
default
Vmem
=
"5G"
override
val
default
CoreMemory
=
4.0
override
val
defaultThreads
=
8
/** Returns command to execute */
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
View file @
9f2940e0
...
...
@@ -69,7 +69,7 @@ class BwaMem(val root: Configurable) extends Bwa {
var
Y
:
Boolean
=
config
(
"Y"
,
default
=
false
)
var
I
:
Option
[
String
]
=
config
(
"I"
)
override
val
default
Vmem
=
"6G"
override
val
default
CoreMemory
=
4.0
override
val
defaultThreads
=
8
def
cmdLine
=
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
View file @
9f2940e0
...
...
@@ -26,7 +26,7 @@ abstract class Conifer extends PythonCommandLineFunction {
override
val
versionExitcode
=
List
(
0
)
override
def
versionCommand
=
executable
+
" "
+
python_script
+
" --version"
override
val
default
Vmem
=
"8G"
override
val
default
CoreMemory
=
5.0
override
val
defaultThreads
=
1
def
cmdLine
=
getPythonCommand
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala
View file @
9f2940e0
...
...
@@ -31,7 +31,7 @@ abstract class Gatk extends BiopetJavaCommandLineFunction {
val
analysisType
:
String
override
val
default
Vmem
=
"5G"
override
val
default
CoreMemory
=
3.0
@Input
(
required
=
true
)
var
reference
:
File
=
config
(
"reference"
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
View file @
9f2940e0
...
...
@@ -59,7 +59,7 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
var
pairs
:
Boolean
=
config
(
"pairs"
,
default
=
false
)
override
val
default
Vmem
=
"6G"
override
val
default
CoreMemory
=
4.0
override
def
beforeGraph
{
super
.
beforeGraph
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
View file @
9f2940e0
...
...
@@ -60,8 +60,7 @@ abstract class Picard extends BiopetJavaCommandLineFunction {
override
val
versionRegex
=
"""Version: (.*)"""
.
r
override
val
versionExitcode
=
List
(
0
,
1
)
override
val
defaultVmem
=
"8G"
memoryLimit
=
Option
(
3.0
)
override
val
defaultCoreMemory
=
3.0
override
def
commandLine
=
super
.
commandLine
+
required
(
"TMP_DIR="
+
jobTempDir
)
+
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
View file @
9f2940e0
...
...
@@ -19,7 +19,7 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
/** General Sambamba extension */
abstract
class
Sambamba
extends
BiopetCommandLineFunction
{
override
val
default
Vmem
=
"4G"
override
val
default
CoreMemory
=
2.0
override
val
defaultThreads
=
2
override
def
subPath
=
"sambamba"
::
super
.
subPath
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Breakdancer.scala
View file @
9f2940e0
...
...
@@ -84,7 +84,7 @@ object BreakdancerConfig {
class
BreakdancerCaller
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
executable
=
config
(
"exe"
,
default
=
"breakdancer-max"
,
freeVar
=
false
)
override
val
default
Vmem
=
"6G"
override
val
default
CoreMemory
=
4.0
override
val
defaultThreads
=
1
// breakdancer can only work on 1 single thread
override
val
versionRegex
=
""".*[Vv]ersion:? (.*)"""
.
r
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Clever.scala
View file @
9f2940e0
...
...
@@ -28,7 +28,7 @@ class Clever(val root: Configurable) extends BiopetCommandLineFunction {
private
lazy
val
versionexecutable
:
File
=
config
(
"version_exe"
,
default
=
(
new
File
(
executable
).
getParent
+
"/ctk-version"
))
override
val
default
Vmem
=
"4G"
override
val
default
CoreMemory
=
3.0
override
val
defaultThreads
=
8
override
def
versionCommand
=
versionexecutable
.
getAbsolutePath
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/pindel/PindelCaller.scala
View file @
9f2940e0
...
...
@@ -23,7 +23,7 @@ import java.io.File
class
PindelCaller
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
executable
=
config
(
"exe"
,
default
=
"pindel"
,
freeVar
=
false
)
override
val
default
Vmem
=
"8G"
override
val
default
CoreMemory
=
5.0
override
val
defaultThreads
=
8
override
val
versionRegex
=
"""Pindel version:? (.*)"""
.
r
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala
View file @
9f2940e0
...
...
@@ -29,7 +29,6 @@ abstract class Varscan extends BiopetJavaCommandLineFunction {
* override val versionRegex = """VarScan v(.*)""".r
*/
override
val
defaultVmem
=
"8G"
memoryLimit
=
Option
(
3.0
)
override
val
defaultCoreMemory
=
5.0
}
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