Fix imports

4e12b4c4 · Peter van 't Hof · 36b53286 · 4e12b4c4 · 4e12b4c4 · 4e12b4c4
Commit 4e12b4c4 authored 9 years ago by Peter van 't Hof
--- a/external-example/pom.xml
+++ b/external-example/pom.xml
@@ -42,6 +42,11 @@
            <!--TODO: replace version of pipeline to a fixed version -->
            <version>0.5.0-SNAPSHOT</version>
        </dependency>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>BiopetExtensions</artifactId>
+            <version>0.5.0-SNAPSHOT</version>
+        </dependency>
        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>Shiva</artifactId>

--- a/external-example/src/main/scala/org/example/group/ExecutableExample.scala
+++ b/external-example/src/main/scala/org/example/group/ExecutableExample.scala
 package org.example.group

-import nl.lumc.sasc.biopet.core.{ MainCommand, BiopetExecutable }
+import nl.lumc.sasc.biopet.utils.{ BiopetExecutable, MainCommand }

 /**
 * Created by pjvanthof on 30/08/15.

--- a/external-example/src/main/scala/org/example/group/pipelines/BiopetPipeline.scala
+++ b/external-example/src/main/scala/org/example/group/pipelines/BiopetPipeline.scala
 package org.example.group.pipelines

 import nl.lumc.sasc.biopet.core.PipelineCommand
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.pipelines.shiva.Shiva
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript

 /**

--- a/external-example/src/main/scala/org/example/group/pipelines/MultisamplePipeline.scala
+++ b/external-example/src/main/scala/org/example/group/pipelines/MultisamplePipeline.scala
 package org.example.group.pipelines

 import nl.lumc.sasc.biopet.core.{ PipelineCommand, MultiSampleQScript }
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript

 /**

--- a/external-example/src/main/scala/org/example/group/pipelines/SimplePipeline.scala
+++ b/external-example/src/main/scala/org/example/group/pipelines/SimplePipeline.scala
 package org.example.group.pipelines

 import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.extensions.{ Gzip, Cat }
 import org.broadinstitute.gatk.queue.QScript