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biopet.biopet
Commits
c0a2280c
Commit
c0a2280c
authored
Mar 04, 2015
by
Peter van 't Hof
Browse files
Switched Basty to Shiva
parent
aab08ec8
Changes
12
Hide whitespace changes
Inline
Side-by-side
protected/biopet-gatk-pipelines/pom.xml
View file @
c0a2280c
...
...
@@ -39,6 +39,11 @@
<artifactId>
Mapping
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Basty
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Shiva
</artifactId>
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Basty.scala
0 → 100644
View file @
c0a2280c
package
nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.core.PipelineCommand
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.pipelines.basty.BastyTrait
import
org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvan_thof on 3/4/15.
*/
class
Basty
(
val
root
:
Configurable
)
extends
QScript
with
BastyTrait
{
qscript
=>
def
this
()
=
this
(
null
)
override
def
variantcallers
=
List
(
"unifiedgenotyper"
)
override
lazy
val
shiva
=
new
Shiva
(
qscript
)
}
object
Basty
extends
PipelineCommand
\ No newline at end of file
protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutableProtected.scala
View file @
c0a2280c
...
...
@@ -11,7 +11,7 @@ object BiopetExecutableProtected extends BiopetExecutable {
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gatk
.
GatkPipeline
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gatk
.
Shiva
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gatk
.
ShivaVariantcalling
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
basty
.
Basty
)
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gatk
.
Basty
)
def
tools
=
BiopetExecutablePublic
.
tools
}
\ No newline at end of file
protected/pom.xml
View file @
c0a2280c
...
...
@@ -20,7 +20,6 @@
<modules>
<module>
biopet-gatk-extensions
</module>
<module>
biopet-gatk-pipelines
</module>
<module>
basty
</module>
<module>
biopet-protected-package
</module>
</modules>
</project>
\ No newline at end of file
p
rotected
/basty/.gitignore
→
p
ublic
/basty/.gitignore
View file @
c0a2280c
File moved
p
rotected
/basty/pom.xml
→
p
ublic
/basty/pom.xml
View file @
c0a2280c
...
...
@@ -31,7 +31,7 @@
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetGatkPipelines
</artifactId>
<artifactId>
Shiva
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
...
...
public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
0 → 100644
View file @
c0a2280c
package
nl.lumc.sasc.biopet.pipelines.basty
import
nl.lumc.sasc.biopet.core.PipelineCommand
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvan_thof on 3/4/15.
*/
class
Basty
(
val
root
:
Configurable
)
extends
QScript
with
BastyTrait
{
def
this
()
=
this
(
null
)
}
object
Basty
extends
PipelineCommand
\ No newline at end of file
p
rotected
/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
→
p
ublic
/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty
Trait
.scala
View file @
c0a2280c
...
...
@@ -8,17 +8,13 @@ package nl.lumc.sasc.biopet.pipelines.basty
import
java.io.File
import
nl.lumc.sasc.biopet.core.MultiSampleQScript
import
nl.lumc.sasc.biopet.core.PipelineCommand
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.
{
RunGubbins
,
Cat
,
Raxml
}
import
nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline
import
nl.lumc.sasc.biopet.pipelines.shiva.Shiva
import
nl.lumc.sasc.biopet.pipelines.shiva.
{
ShivaTrait
,
Shiva
}
import
nl.lumc.sasc.biopet.tools.BastyGenerateFasta
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
org.broadinstitute.gatk.queue.QScript
class
Basty
(
val
root
:
Configurable
)
extends
QScript
with
MultiSampleQScript
{
trait
Basty
Trait
extends
MultiSampleQScript
{
qscript
=>
def
this
()
=
this
(
null
)
case
class
FastaOutput
(
variants
:
File
,
consensus
:
File
,
consensusVariants
:
File
)
...
...
@@ -26,10 +22,10 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
override
def
defaults
=
ConfigUtils
.
mergeMaps
(
Map
(
"ploidy"
->
1
,
"variant
s
callers"
->
variantcallers
"variantcallers"
->
variantcallers
),
super
.
defaults
)
val
shiva
=
new
Shiva
(
qscript
)
lazy
val
shiva
:
ShivaTrait
=
new
Shiva
(
qscript
)
def
summaryFile
:
File
=
new
File
(
outputDir
,
"Sage.summary.json"
)
...
...
@@ -114,7 +110,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
val
raxmlMl
=
new
Raxml
(
this
)
raxmlMl
.
input
=
variants
raxmlMl
.
m
=
config
(
"raxml_ml_model"
,
default
=
"GTRGAMMAX"
)
raxmlMl
.
p
=
seed
raxmlMl
.
p
=
Some
(
seed
)
raxmlMl
.
n
=
outputName
+
"_ml"
raxmlMl
.
w
=
dirSufixRaxml
raxmlMl
.
N
=
config
(
"ml_runs"
,
default
=
20
,
submodule
=
"raxml"
)
...
...
@@ -127,10 +123,10 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
raxmlBoot
.
threads
=
1
raxmlBoot
.
input
=
variants
raxmlBoot
.
m
=
config
(
"raxml_ml_model"
,
default
=
"GTRGAMMAX"
)
raxmlBoot
.
p
=
seed
raxmlBoot
.
b
=
math
.
abs
(
r
.
nextInt
)
raxmlBoot
.
p
=
Some
(
seed
)
raxmlBoot
.
b
=
Some
(
math
.
abs
(
r
.
nextInt
)
)
raxmlBoot
.
w
=
dirSufixRaxml
raxmlBoot
.
N
=
1
raxmlBoot
.
N
=
Some
(
1
)
raxmlBoot
.
n
=
outputName
+
"_boot_"
+
t
add
(
raxmlBoot
)
raxmlBoot
.
getBootstrapFile
...
...
@@ -144,7 +140,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
raxmlBi
.
t
=
raxmlMl
.
getBestTreeFile
raxmlBi
.
z
=
cat
.
output
raxmlBi
.
m
=
config
(
"raxml_ml_model"
,
default
=
"GTRGAMMAX"
)
raxmlBi
.
p
=
seed
raxmlBi
.
p
=
Some
(
seed
)
raxmlBi
.
f
=
"b"
raxmlBi
.
n
=
outputName
+
"_bi"
raxmlBi
.
w
=
dirSufixRaxml
...
...
@@ -181,5 +177,3 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
return
FastaOutput
(
bastyGenerateFasta
.
outputVariants
,
bastyGenerateFasta
.
outputConsensus
,
bastyGenerateFasta
.
outputConsensusVariants
)
}
}
object
Basty
extends
PipelineCommand
p
rotected
/basty/src/test/resources/log4j.properties
→
p
ublic
/basty/src/test/resources/log4j.properties
View file @
c0a2280c
File moved
public/biopet-public-package/pom.xml
View file @
c0a2280c
...
...
@@ -100,6 +100,11 @@
<artifactId>
Shiva
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Basty
</artifactId>
<version>
${project.version}
</version>
</dependency>
</dependencies>
<build>
<plugins>
...
...
public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala
View file @
c0a2280c
...
...
@@ -31,7 +31,8 @@ object BiopetExecutablePublic extends BiopetExecutable {
def
pipelines
:
List
[
MainCommand
]
=
List
(
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
shiva
.
Shiva
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
shiva
.
ShivaVariantcalling
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
shiva
.
ShivaVariantcalling
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
basty
.
Basty
)
:::
protectedPipelines
def
tools
:
List
[
MainCommand
]
=
List
(
...
...
public/pom.xml
View file @
c0a2280c
...
...
@@ -38,6 +38,7 @@
<module>
carp
</module>
<module>
toucan
</module>
<module>
shiva
</module>
<module>
basty
</module>
</modules>
<properties>
...
...
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