From 7d112c68d0182cfe7b8c9e0d020f3f08551802da Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sun, 13 Sep 2015 12:40:49 +0200
Subject: [PATCH] Rscript usable without core now
---
.../bammetrics/BammetricsReport.scala | 2 +-
.../rscript/plotScatter.R | 0
.../{extensions => utils}/rscript/plotXY.R | 0
.../rscript/stackedBar.R | 0
.../PythonCommandLineFunction.scala | 2 +-
.../RscriptCommandLineFunction.scala | 65 ++-----------------
.../nl/lumc/sasc/biopet/tools/plotHeatmap.R | 0
.../sasc/biopet/tools/RegionAfCount.scala | 2 +-
.../sasc/biopet/tools/SummaryToTsvTest.scala | 2 +-
.../sasc/biopet/utils}/rscript/plotScatter.R | 0
.../lumc/sasc/biopet/utils}/rscript/plotXY.R | 0
.../sasc/biopet/utils}/rscript/stackedBar.R | 0
.../sasc/biopet/utils}/rscript/LinePlot.scala | 28 ++++----
.../sasc/biopet/utils/rscript/Rscript.scala | 65 +++++++++++++++++++
.../biopet/utils}/rscript/ScatterPlot.scala | 28 ++++----
.../utils}/rscript/StackedBarPlot.scala | 26 ++++----
.../pipelines/flexiprep/FlexiprepReport.scala | 2 +-
.../biopet/pipelines/shiva/ShivaReport.scala | 2 +-
18 files changed, 112 insertions(+), 112 deletions(-)
rename public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/{extensions => utils}/rscript/plotScatter.R (100%)
rename public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/{extensions => utils}/rscript/plotXY.R (100%)
rename public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/{extensions => utils}/rscript/stackedBar.R (100%)
rename public/{biopet-framework => biopet-tools}/src/main/resources/nl/lumc/sasc/biopet/tools/plotHeatmap.R (100%)
rename public/{biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions => biopet-utils/src/main/resources/nl/lumc/sasc/biopet/utils}/rscript/plotScatter.R (100%)
rename public/{biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions => biopet-utils/src/main/resources/nl/lumc/sasc/biopet/utils}/rscript/plotXY.R (100%)
rename public/{biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions => biopet-utils/src/main/resources/nl/lumc/sasc/biopet/utils}/rscript/stackedBar.R (100%)
rename public/{biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions => biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils}/rscript/LinePlot.scala (67%)
create mode 100644 public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala
rename public/{biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions => biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils}/rscript/ScatterPlot.scala (67%)
rename public/{biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions => biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils}/rscript/StackedBarPlot.scala (68%)
diff --git a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
index b12fafa83..4ebf2ed83 100644
--- a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+++ b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
@@ -20,7 +20,7 @@ import java.io.{ File, PrintWriter }
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportBuilder, ReportPage, ReportSection }
import nl.lumc.sasc.biopet.core.summary.{ Summary, SummaryValue }
-import nl.lumc.sasc.biopet.extensions.rscript.{ StackedBarPlot, LinePlot }
+import nl.lumc.sasc.biopet.utils.rscript.{ StackedBarPlot, LinePlot }
class BammetricsReport(val root: Configurable) extends ReportBuilderExtension {
val builder = BammetricsReport
diff --git a/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/plotScatter.R b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotScatter.R
similarity index 100%
rename from public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/plotScatter.R
rename to public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotScatter.R
diff --git a/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/plotXY.R b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotXY.R
similarity index 100%
rename from public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/plotXY.R
rename to public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotXY.R
diff --git a/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/stackedBar.R b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/stackedBar.R
similarity index 100%
rename from public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/stackedBar.R
rename to public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/stackedBar.R
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala
index 000c77a9a..044b43676 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala
@@ -15,7 +15,7 @@
*/
package nl.lumc.sasc.biopet.core.extensions
-import java.io.{File, FileOutputStream}
+import java.io.{ File, FileOutputStream }
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.Input
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/RscriptCommandLineFunction.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/RscriptCommandLineFunction.scala
index cce714ef1..c773de615 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/RscriptCommandLineFunction.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/RscriptCommandLineFunction.scala
@@ -15,9 +15,10 @@
*/
package nl.lumc.sasc.biopet.core.extensions
-import java.io.{File, FileOutputStream}
+import java.io.{ File, FileOutputStream }
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.utils.rscript.Rscript
import scala.sys.process._
@@ -26,67 +27,13 @@ import scala.sys.process._
*
* Created by wyleung on 17-2-15.
*/
-trait RscriptCommandLineFunction extends BiopetCommandLineFunction {
+trait RscriptCommandLineFunction extends BiopetCommandLineFunction with Rscript {
- protected var script: File
-
- executable = config("exe", default = "Rscript", submodule = "Rscript")
+ executable = rscriptExecutable
override def beforeGraph(): Unit = {
- checkScript()
- }
-
- /**
- * If script not exist in file system it try to copy it from the jar
- * @param local if true it use File.createTempFile instead of ".queue/tmp/"
- */
- protected def checkScript(local: Boolean = false): Unit = {
- if (script.exists()) {
- script = script.getAbsoluteFile
- } else {
- val rScript: File = {
- if (local) File.createTempFile(script.getName, ".R")
- else new File(".queue/tmp/" + script)
- }
- if (!rScript.getParentFile.exists) rScript.getParentFile.mkdirs
-
- val is = getClass.getResourceAsStream(script.getPath)
- val os = new FileOutputStream(rScript)
-
- org.apache.commons.io.IOUtils.copy(is, os)
- os.close()
-
- script = rScript
- }
+ checkScript(Some(jobTempDir))
}
- /**
- * Execute rscript on local system
- * @param logger How to handle stdout and stderr
- */
- def runLocal(logger: ProcessLogger): Unit = {
- checkScript(local = true)
-
- this.logger.info(cmdLine)
-
- val cmd = cmdLine.stripPrefix(" '").stripSuffix("' ").split("' *'")
-
- this.logger.info(cmd.mkString(" "))
-
- val process = Process(cmd.toSeq).run(logger)
- this.logger.info(process.exitValue())
- }
-
- /**
- * Execute rscript on local system
- * Stdout and stderr will go to biopet logger
- */
- def runLocal(): Unit = {
- runLocal(ProcessLogger(logger.info(_)))
- }
-
- def cmdLine: String = {
- required(executable) +
- required(script)
- }
+ def cmdLine: String = repeat(cmd)
}
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/tools/plotHeatmap.R b/public/biopet-tools/src/main/resources/nl/lumc/sasc/biopet/tools/plotHeatmap.R
similarity index 100%
rename from public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/tools/plotHeatmap.R
rename to public/biopet-tools/src/main/resources/nl/lumc/sasc/biopet/tools/plotHeatmap.R
diff --git a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
index 6f1c72a55..66d7f3250 100644
--- a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
@@ -19,7 +19,7 @@ import java.io.{ PrintWriter, InputStream, File }
import java.util
import htsjdk.variant.vcf.VCFFileReader
-import nl.lumc.sasc.biopet.extensions.rscript.ScatterPlot
+import nl.lumc.sasc.biopet.utils.rscript.ScatterPlot
import nl.lumc.sasc.biopet.utils.intervals.{ BedRecord, BedRecordList }
import scala.collection.JavaConversions._
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
index 916fd48cc..6071fceaa 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
@@ -9,7 +9,7 @@ import org.scalatest.mock.MockitoSugar
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.Test
-import nl.lumc.sasc.biopet.core.summary.Summary
+import nl.lumc.sasc.biopet.utils.summary.Summary
/**
* Created by ahbbollen on 31-8-15.
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/plotScatter.R b/public/biopet-utils/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotScatter.R
similarity index 100%
rename from public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/plotScatter.R
rename to public/biopet-utils/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotScatter.R
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/plotXY.R b/public/biopet-utils/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotXY.R
similarity index 100%
rename from public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/plotXY.R
rename to public/biopet-utils/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotXY.R
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/stackedBar.R b/public/biopet-utils/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/stackedBar.R
similarity index 100%
rename from public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/stackedBar.R
rename to public/biopet-utils/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/stackedBar.R
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/LinePlot.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/LinePlot.scala
similarity index 67%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/LinePlot.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/LinePlot.scala
index 4ff413b1f..fb0e2f0a0 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/LinePlot.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/LinePlot.scala
@@ -13,26 +13,22 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.extensions.rscript
+package nl.lumc.sasc.biopet.utils.rscript
import java.io.File
-import nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Extension for en general line plot with R
*
* Created by pjvan_thof on 4/29/15.
*/
-class LinePlot(val root: Configurable) extends RscriptCommandLineFunction {
+class LinePlot(val root: Configurable) extends Rscript {
protected var script: File = config("script", default = "plotXY.R")
- @Input
var input: File = _
- @Output
var output: File = _
var width: Option[Int] = config("width")
@@ -43,14 +39,14 @@ class LinePlot(val root: Configurable) extends RscriptCommandLineFunction {
var title: Option[String] = config("title")
var removeZero: Boolean = config("removeZero", default = false)
- override def cmdLine: String = super.cmdLine +
- required("--input", input) +
- required("--output", output) +
- optional("--width", width) +
- optional("--height", height) +
- optional("--xlabel", xlabel) +
- required("--ylabel", ylabel) +
- optional("--llabel", llabel) +
- optional("--title", title) +
- optional("--removeZero", removeZero)
+ override def cmd = super.cmd ++
+ Seq("--input", input.getAbsolutePath) ++
+ Seq("--output", output.getAbsolutePath) ++
+ width.map(x => Seq("--width", x.toString)).getOrElse(Seq()) ++
+ height.map(x => Seq("--height", x.toString)).getOrElse(Seq()) ++
+ xlabel.map(Seq("--xlabel", _)).getOrElse(Seq()) ++
+ ylabel.map(Seq("--ylabel", _)).getOrElse(Seq()) ++
+ llabel.map(Seq("--llabel", _)).getOrElse(Seq()) ++
+ title.map(Seq("--title", _)).getOrElse(Seq()) ++
+ (if (removeZero) Seq("--removeZero") else Seq())
}
diff --git a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala
new file mode 100644
index 000000000..685108d0c
--- /dev/null
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala
@@ -0,0 +1,65 @@
+package nl.lumc.sasc.biopet.utils.rscript
+
+import java.io.{ File, FileOutputStream }
+
+import nl.lumc.sasc.biopet.utils.Logging
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+import scala.sys.process.{ Process, ProcessLogger }
+
+/**
+ * Created by pjvanthof on 13/09/15.
+ */
+trait Rscript extends Configurable {
+ protected var script: File
+
+ def rscriptExecutable: String = config("exe", default = "Rscript", submodule = "Rscript")
+
+ /** This is the defaul implementation, to add arguments override this */
+ def cmd: Seq[String] = Seq(rscriptExecutable, script.getAbsolutePath)
+
+ /**
+ * If script not exist in file system it try to copy it from the jar
+ * @param dir Directory to store temp script, if None or not given File.createTempFile is called
+ */
+ protected def checkScript(dir: Option[File] = None): Unit = {
+ if (script.exists()) {
+ script = script.getAbsoluteFile
+ } else {
+ val rScript: File = dir match {
+ case Some(dir) => new File(dir, script.getName)
+ case _ => File.createTempFile(script.getName, ".R")
+ }
+ if (!rScript.getParentFile.exists) rScript.getParentFile.mkdirs
+
+ val is = getClass.getResourceAsStream(script.getPath)
+ val os = new FileOutputStream(rScript)
+
+ org.apache.commons.io.IOUtils.copy(is, os)
+ os.close()
+
+ script = rScript
+ }
+ }
+
+ /**
+ * Execute rscript on local system
+ * @param logger How to handle stdout and stderr
+ */
+ def runLocal(logger: ProcessLogger): Unit = {
+ checkScript()
+
+ Logging.logger.info("Running: " + cmd.mkString(" "))
+
+ val process = Process(cmd).run(logger)
+ Logging.logger.info(process.exitValue())
+ }
+
+ /**
+ * Execute rscript on local system
+ * Stdout and stderr will go to biopet logger
+ */
+ def runLocal(): Unit = {
+ runLocal(ProcessLogger(Logging.logger.info(_)))
+ }
+}
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/ScatterPlot.scala
similarity index 67%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/ScatterPlot.scala
index ad3533ced..9bcbaffcc 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/ScatterPlot.scala
@@ -13,26 +13,22 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.extensions.rscript
+package nl.lumc.sasc.biopet.utils.rscript
import java.io.File
-import nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Extension for en general line plot with R
*
* Created by pjvan_thof on 4/29/15.
*/
-class ScatterPlot(val root: Configurable) extends RscriptCommandLineFunction {
+class ScatterPlot(val root: Configurable) extends Rscript {
protected var script: File = config("script", default = "plotScatter.R")
- @Input
var input: File = _
- @Output
var output: File = _
var width: Option[Int] = config("width")
@@ -43,14 +39,14 @@ class ScatterPlot(val root: Configurable) extends RscriptCommandLineFunction {
var title: Option[String] = config("title")
var removeZero: Boolean = config("removeZero", default = false)
- override def cmdLine: String = super.cmdLine +
- required("--input", input) +
- required("--output", output) +
- optional("--width", width) +
- optional("--height", height) +
- optional("--xlabel", xlabel) +
- required("--ylabel", ylabel) +
- optional("--llabel", llabel) +
- optional("--title", title) +
- optional("--removeZero", removeZero)
+ override def cmd = super.cmd ++
+ Seq("--input", input.getAbsolutePath) ++
+ Seq("--output", output.getAbsolutePath) ++
+ width.map(x => Seq("--width", x.toString)).getOrElse(Seq()) ++
+ height.map(x => Seq("--height", x.toString)).getOrElse(Seq()) ++
+ xlabel.map(Seq("--xlabel", _)).getOrElse(Seq()) ++
+ ylabel.map(Seq("--ylabel", _)).getOrElse(Seq()) ++
+ llabel.map(Seq("--llabel", _)).getOrElse(Seq()) ++
+ title.map(Seq("--title", _)).getOrElse(Seq()) ++
+ (if (removeZero) Seq("--removeZero") else Seq())
}
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/StackedBarPlot.scala
similarity index 68%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/StackedBarPlot.scala
index 2bf533f81..1965e0a54 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/StackedBarPlot.scala
@@ -13,26 +13,22 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.extensions.rscript
+package nl.lumc.sasc.biopet.utils.rscript
import java.io.File
-import nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Extension for en general stackedbar plot with R
*
* Created by pjvan_thof on 4/29/15.
*/
-class StackedBarPlot(val root: Configurable) extends RscriptCommandLineFunction {
+class StackedBarPlot(val root: Configurable) extends Rscript {
protected var script: File = config("script", default = "stackedBar.R")
- @Input
var input: File = _
- @Output
var output: File = _
var width: Option[Int] = config("width")
@@ -42,13 +38,13 @@ class StackedBarPlot(val root: Configurable) extends RscriptCommandLineFunction
var llabel: Option[String] = config("llabel")
var title: Option[String] = config("title")
- override def cmdLine: String = super.cmdLine +
- required("--input", input) +
- required("--output", output) +
- optional("--width", width) +
- optional("--height", height) +
- optional("--xlabel", xlabel) +
- required("--ylabel", ylabel) +
- optional("--llabel", llabel) +
- optional("--title", title)
+ override def cmd = super.cmd ++
+ Seq("--input", input.getAbsolutePath) ++
+ Seq("--output", output.getAbsolutePath) ++
+ width.map(x => Seq("--width", x.toString)).getOrElse(Seq()) ++
+ height.map(x => Seq("--height", x.toString)).getOrElse(Seq()) ++
+ xlabel.map(Seq("--xlabel", _)).getOrElse(Seq()) ++
+ ylabel.map(Seq("--ylabel", _)).getOrElse(Seq()) ++
+ llabel.map(Seq("--llabel", _)).getOrElse(Seq()) ++
+ title.map(Seq("--title", _)).getOrElse(Seq())
}
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
index e8a0653d9..c435504ca 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
@@ -20,7 +20,7 @@ import java.io.{ File, PrintWriter }
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportBuilder, ReportPage, ReportSection }
import nl.lumc.sasc.biopet.core.summary.{ Summary, SummaryValue }
-import nl.lumc.sasc.biopet.extensions.rscript.StackedBarPlot
+import nl.lumc.sasc.biopet.utils.rscript.StackedBarPlot
class FlexiprepReport(val root: Configurable) extends ReportBuilderExtension {
val builder = FlexiprepReport
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
index 4f47abcca..3f121092d 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
@@ -20,7 +20,7 @@ import java.io.{ File, PrintWriter }
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.report._
import nl.lumc.sasc.biopet.core.summary.{ Summary, SummaryValue }
-import nl.lumc.sasc.biopet.extensions.rscript.StackedBarPlot
+import nl.lumc.sasc.biopet.utils.rscript.StackedBarPlot
import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
--
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