From 4e12b4c47ba0a950f492ff7d79f48dd9f15bca4f Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 18 Sep 2015 10:43:55 +0200
Subject: [PATCH] Fix imports
---
external-example/pom.xml | 5 +++++
.../src/main/scala/org/example/group/ExecutableExample.scala | 2 +-
.../scala/org/example/group/pipelines/BiopetPipeline.scala | 3 ++-
.../org/example/group/pipelines/MultisamplePipeline.scala | 3 ++-
.../scala/org/example/group/pipelines/SimplePipeline.scala | 2 +-
5 files changed, 11 insertions(+), 4 deletions(-)
diff --git a/external-example/pom.xml b/external-example/pom.xml
index 99f1423ec..da0d2258f 100644
--- 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>
diff --git a/external-example/src/main/scala/org/example/group/ExecutableExample.scala b/external-example/src/main/scala/org/example/group/ExecutableExample.scala
index 9e4371322..fe0aaa13d 100644
--- a/external-example/src/main/scala/org/example/group/ExecutableExample.scala
+++ b/external-example/src/main/scala/org/example/group/ExecutableExample.scala
@@ -1,6 +1,6 @@
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.
diff --git a/external-example/src/main/scala/org/example/group/pipelines/BiopetPipeline.scala b/external-example/src/main/scala/org/example/group/pipelines/BiopetPipeline.scala
index bb1d26773..6099047a6 100644
--- a/external-example/src/main/scala/org/example/group/pipelines/BiopetPipeline.scala
+++ b/external-example/src/main/scala/org/example/group/pipelines/BiopetPipeline.scala
@@ -1,9 +1,10 @@
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
/**
diff --git a/external-example/src/main/scala/org/example/group/pipelines/MultisamplePipeline.scala b/external-example/src/main/scala/org/example/group/pipelines/MultisamplePipeline.scala
index fe29ff74b..ee66d8966 100644
--- a/external-example/src/main/scala/org/example/group/pipelines/MultisamplePipeline.scala
+++ b/external-example/src/main/scala/org/example/group/pipelines/MultisamplePipeline.scala
@@ -1,7 +1,8 @@
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
/**
diff --git a/external-example/src/main/scala/org/example/group/pipelines/SimplePipeline.scala b/external-example/src/main/scala/org/example/group/pipelines/SimplePipeline.scala
index caa058d30..f24b0f615 100644
--- a/external-example/src/main/scala/org/example/group/pipelines/SimplePipeline.scala
+++ b/external-example/src/main/scala/org/example/group/pipelines/SimplePipeline.scala
@@ -1,7 +1,7 @@
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
--
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