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biopet.biopet
Commits
3c489130
Commit
3c489130
authored
Jan 19, 2017
by
Sander Bollen
Committed by
GitHub
Jan 19, 2017
Browse files
Merge pull request #7 from biopet/fix-BIOPET-500
Fix BIOPET-500
parents
31be1177
7f01b3a5
Changes
6
Hide whitespace changes
Inline
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.gitmodules
0 → 100644
View file @
3c489130
[submodule "gatk"]
path = gatk
url = https://github.com/biopet/gatk.git
Jenkinsfile
0 → 100644
View file @
3c489130
node
(
'local'
)
{
try
{
stage
(
'Init'
)
{
tool
'JDK 8u102'
tool
'Apache Maven 3.3.9'
}
stage
(
'Checkout'
)
{
checkout
scm
sh
'git submodule update --init --recursive'
}
stage
(
'Build and Test'
)
{
withMaven
(
maven:
'Apache Maven 3.3.9'
,
jdk:
'JDK 8u102'
)
{
sh
'mvn -B -T 2 -Dmaven.test.failure.ignore clean package'
}
}
stage
(
'Report tests'
)
{
junit
'*/target/surefire-reports/*.xml'
}
if
(
currentBuild
.
result
==
null
||
"SUCCESS"
.
equals
(
currentBuild
.
result
))
{
currentBuild
.
result
=
"SUCCESS"
slackSend
(
color:
'#00FF00'
,
message:
"${currentBuild.result}: Job '${env.JOB_NAME} #${env.BUILD_NUMBER}' (<${env.BUILD_URL}|Open>)"
,
channel:
'#biopet-bot'
,
teamDomain:
'lumc'
,
tokenCredentialId:
'lumc'
)
}
else
{
slackSend
(
color:
'#FFFF00'
,
message:
"${currentBuild.result}: Job '${env.JOB_NAME} #${env.BUILD_NUMBER}' (<${env.BUILD_URL}|Open>)"
,
channel:
'#biopet-bot'
,
teamDomain:
'lumc'
,
tokenCredentialId:
'lumc'
)
}
}
catch
(
e
)
{
if
(
currentBuild
.
result
==
null
||
"FAILED"
.
equals
(
currentBuild
.
result
))
{
currentBuild
.
result
=
"FAILED"
}
slackSend
(
color:
'#FF0000'
,
message:
"${currentBuild.result}: Job '${env.JOB_NAME} #${env.BUILD_NUMBER}' (<${env.BUILD_URL}|Open>)"
,
channel:
'#biopet-bot'
,
teamDomain:
'lumc'
,
tokenCredentialId:
'lumc'
)
throw
e
}
}
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
View file @
3c489130
...
...
@@ -47,6 +47,11 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
private
def
changeScript
(
file
:
File
)
:
Unit
=
{
val
lines
=
Source
.
fromFile
(
file
).
getLines
().
toList
val
writer
=
new
PrintWriter
(
file
)
remoteCommand
match
{
case
"bash"
=>
writer
.
println
(
"#!/bin/bash"
)
case
"sh"
=>
writer
.
println
(
"#!/bin/sh"
)
case
_
=>
writer
.
println
(
s
"#!$remoteCommand"
)
}
writer
.
println
(
"set -eubf"
)
writer
.
println
(
"set -o pipefail"
)
lines
.
foreach
(
writer
.
println
)
...
...
@@ -66,8 +71,9 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
changeScript
(
new
File
(
jt
.
getArgs
.
head
.
toString
))
jt
.
setRemoteCommand
(
remoteCommand
)
case
ps
:
ProcessSettings
=>
changeScript
(
new
File
(
ps
.
getCommand
.
tail
.
head
))
ps
.
setCommand
(
Array
(
remoteCommand
)
++
ps
.
getCommand
.
tail
)
changeScript
(
new
File
(
ps
.
getCommand
.
last
))
if
(
ps
.
getCommand
.
head
!=
"srun"
)
ps
.
setCommand
(
Array
(
remoteCommand
)
++
ps
.
getCommand
.
tail
)
}
/**
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala
View file @
3c489130
...
...
@@ -48,14 +48,19 @@ trait CommandLineResources extends CommandLineFunction with Configurable {
def
coreMemory
=
_coreMemory
/** This value is for SGE and is defined in seconds */
protected
val
maxWalltimeLimit
:
Option
[
Int
]
=
config
(
"max_walltime_limit"
)
wallTime
=
config
(
"max_walltime"
)
/** This value is specific for slurm */
qualityOfSerice
=
config
(
"quality_of_serice"
)
var
retry
=
0
override
def
freezeFieldValues
()
:
Unit
=
{
setResources
()
if
(
useSge
&&
vmem
.
isDefined
)
jobResourceRequests
:+=
s
"h_vmem=${vmem.get}"
if
(
useSge
&&
maxWalltimeLimit
.
isDefined
)
jobResourceRequests
:+=
s
"h_rt=${maxWalltimeLimit.get}"
if
(
useSge
)
{
vmem
.
foreach
(
v
=>
jobResourceRequests
:+=
s
"h_vmem=$v"
)
wallTime
.
foreach
(
t
=>
jobResourceRequests
:+=
s
"h_rt=$t"
)
}
super
.
freezeFieldValues
()
}
...
...
@@ -106,6 +111,7 @@ trait CommandLineResources extends CommandLineFunction with Configurable {
if
(
vmem
.
isDefined
)
jobResourceRequests
=
jobResourceRequests
.
filterNot
(
_
.
contains
(
"h_vmem="
))
if
(
retry
>
0
)
logger
.
info
(
"Auto raise memory on retry"
)
retry
+=
1
waitBeforeJob
=
waitBeforeJob
.
map
(
_
+
(
retry
*
10
))
this
.
freezeFieldValues
()
}
...
...
@@ -117,8 +123,8 @@ trait CommandLineResources extends CommandLineFunction with Configurable {
_coreMemory
=
commands
.
map
(
cmd
=>
cmd
.
coreMemory
*
(
cmd
.
threads
.
toDouble
/
threads
.
toDouble
)).
sum
memoryLimit
=
Some
(
_coreMemory
*
threads
)
residentLimit
=
Some
((
_coreMemory
+
(
0.5
*
retry
))
*
residentFactor
)
vmem
=
Some
((
_coreMemory
*
(
vmemFactor
+
(
0.5
*
retry
)))
+
"G"
)
residentLimit
=
Some
((
_coreMemory
+
(
0.5
*
retry
))
*
residentFactor
*
(
if
(
multiplyRssThreads
)
threads
else
1
)
)
vmem
=
Some
((
_coreMemory
*
(
vmemFactor
+
(
0.5
*
retry
))
*
(
if
(
multiplyVmemThreads
)
threads
else
1
)
)
+
"G"
)
}
}
gatk
@
7805065f
Subproject commit 7805065f00df24c58948ea9961a4e9393ae64c70
pom.xml
View file @
3c489130
...
...
@@ -24,6 +24,7 @@
<version>
0.8.0-SNAPSHOT
</version>
<modules>
<module>
gatk
</module>
<module>
biopet-package
</module>
<module>
bam2wig
</module>
<module>
bammetrics
</module>
...
...
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