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biopet.biopet
Commits
3dc3aad4
Commit
3dc3aad4
authored
Mar 26, 2015
by
Peter van 't Hof
Browse files
Switch to scala 2.10
parent
04f35d97
Changes
9
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protected/biopet-gatk-pipelines/pom.xml
View file @
3dc3aad4
...
...
@@ -57,7 +57,7 @@
</dependency>
<dependency>
<groupId>
org.scalatest
</groupId>
<artifactId>
scalatest_2.1
1
</artifactId>
<artifactId>
scalatest_2.1
0
</artifactId>
<version>
2.2.1
</version>
<scope>
test
</scope>
</dependency>
...
...
public/biopet-framework/pom.xml
View file @
3dc3aad4
...
...
@@ -55,14 +55,14 @@
</dependency>
<dependency>
<groupId>
org.scalatest
</groupId>
<artifactId>
scalatest_2.1
1
</artifactId>
<artifactId>
scalatest_2.1
0
</artifactId>
<version>
2.2.1
</version>
<scope>
test
</scope>
</dependency>
<dependency>
<groupId>
org.scala-lang
</groupId>
<artifactId>
scala-library
</artifactId>
<version>
2.1
1
.2
</version>
<version>
2.1
0
.2
</version>
</dependency>
<dependency>
<groupId>
org.broadinstitute.gatk
</groupId>
...
...
@@ -87,7 +87,7 @@
</dependency>
<dependency>
<groupId>
io.argonaut
</groupId>
<artifactId>
argonaut_2.1
1
</artifactId>
<artifactId>
argonaut_2.1
0
</artifactId>
<version>
6.1-M4
</version>
</dependency>
<dependency>
...
...
@@ -110,5 +110,10 @@
<artifactId>
scopt_2.10
</artifactId>
<version>
3.3.0
</version>
</dependency>
<dependency>
<groupId>
org.scalatra.scalate
</groupId>
<artifactId>
scalate-core_2.10
</artifactId>
<version>
1.7.0
</version>
</dependency>
</dependencies>
</project>
public/carp/pom.xml
View file @
3dc3aad4
...
...
@@ -52,7 +52,7 @@
</dependency>
<dependency>
<groupId>
org.scalatest
</groupId>
<artifactId>
scalatest_2.1
1
</artifactId>
<artifactId>
scalatest_2.1
0
</artifactId>
<version>
2.2.1
</version>
<scope>
test
</scope>
</dependency>
...
...
public/flexiprep/pom.xml
View file @
3dc3aad4
...
...
@@ -47,7 +47,7 @@
</dependency>
<dependency>
<groupId>
org.scalatest
</groupId>
<artifactId>
scalatest_2.1
1
</artifactId>
<artifactId>
scalatest_2.1
0
</artifactId>
<version>
2.2.1
</version>
<scope>
test
</scope>
</dependency>
...
...
public/gentrap/pom.xml
View file @
3dc3aad4
...
...
@@ -52,7 +52,7 @@
</dependency>
<dependency>
<groupId>
org.scalatest
</groupId>
<artifactId>
scalatest_2.1
1
</artifactId>
<artifactId>
scalatest_2.1
0
</artifactId>
<version>
2.2.1
</version>
<scope>
test
</scope>
</dependency>
...
...
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/CufflinksProducer.scala
View file @
3dc3aad4
...
...
@@ -21,12 +21,17 @@ import scalaz._, Scalaz._
import
nl.lumc.sasc.biopet.extensions.
{
Cufflinks
,
Ln
}
/** General trait for containing cufflinks results */
trait
CufflinksProducer
{
this:
Gentrap
#
Sample
=>
trait
CufflinksProducer
{
import
Gentrap._
import
Gentrap.ExpMeasures._
import
Gentrap.StrandProtocol._
protected
def
sampleDir
:
File
protected
def
sampleId
:
String
protected
def
pipeline
:
Gentrap
protected
def
alnFile
:
File
/** Valid cufflink measure types */
protected
val
cufflinksMeasures
=
Set
(
CufflinksStrict
,
CufflinksGuided
,
CufflinksBlind
)
...
...
public/mapping/pom.xml
View file @
3dc3aad4
...
...
@@ -57,7 +57,7 @@
</dependency>
<dependency>
<groupId>
org.scalatest
</groupId>
<artifactId>
scalatest_2.1
1
</artifactId>
<artifactId>
scalatest_2.1
0
</artifactId>
<version>
2.2.1
</version>
<scope>
test
</scope>
</dependency>
...
...
public/pom.xml
View file @
3dc3aad4
...
...
@@ -210,7 +210,7 @@
<artifactId>
scoverage-maven-plugin
</artifactId>
<version>
${scoverage.plugin.version}
</version>
<configuration>
<scalaVersion>
2.1
1.4
</scalaVersion>
<scalaVersion>
2.1
0.2
</scalaVersion>
<!-- other parameters -->
</configuration>
</plugin>
...
...
public/shiva/pom.xml
View file @
3dc3aad4
...
...
@@ -48,7 +48,7 @@
</dependency>
<dependency>
<groupId>
org.scalatest
</groupId>
<artifactId>
scalatest_2.1
1
</artifactId>
<artifactId>
scalatest_2.1
0
</artifactId>
<version>
2.2.1
</version>
<scope>
test
</scope>
</dependency>
...
...
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