Added a tool package

protected/biopet-protected-package/pom.xml

@@ -24,7 +24,7 @@
 
     <properties>
         <sting.shade.phase>package</sting.shade.phase>
-        <app.main.class>nl.lumc.sasc.biopet.core.BiopetExecutableProtected</app.main.class>
+        <app.main.class>nl.lumc.sasc.biopet.BiopetExecutableProtected</app.main.class>
     </properties>
 
     <dependencies>

protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutableProtected.scala

@@ -5,8 +5,7 @@
  */
 package nl.lumc.sasc.biopet
 
-import nl.lumc.sasc.biopet.core.BiopetExecutable
-import nl.lumc.sasc.biopet.utils.MainCommand
+import nl.lumc.sasc.biopet.utils.{BiopetExecutable, MainCommand}
 
 object BiopetExecutableProtected extends BiopetExecutable {
   def pipelines: List[MainCommand] = BiopetExecutablePublic.pipelines ::: List(

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala

@@ -17,9 +17,8 @@ package nl.lumc.sasc.biopet.core.report
 
 import java.io._
 import nl.lumc.sasc.biopet.core.ToolCommandFuntion
-import nl.lumc.sasc.biopet.tools.ToolCommand
 import nl.lumc.sasc.biopet.utils.summary.Summary
-import nl.lumc.sasc.biopet.utils.{ Logging, IoUtils }
+import nl.lumc.sasc.biopet.utils.{ ToolCommand, Logging, IoUtils }
 import org.broadinstitute.gatk.utils.commandline.Input
 import org.fusesource.scalate.{ TemplateEngine, TemplateSource }
 import scala.collection.mutable

public/biopet-public-package/pom.xml

@@ -35,7 +35,7 @@
 
     <properties>
         <sting.shade.phase>package</sting.shade.phase>
-        <app.main.class>nl.lumc.sasc.biopet.core.BiopetExecutablePublic</app.main.class>
+        <app.main.class>nl.lumc.sasc.biopet.BiopetExecutablePublic</app.main.class>
     </properties>
 
     <dependencies>

public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala

@@ -15,8 +15,7 @@
  */
 package nl.lumc.sasc.biopet
 
-import nl.lumc.sasc.biopet.core.BiopetExecutable
-import nl.lumc.sasc.biopet.utils.MainCommand
+import nl.lumc.sasc.biopet.utils.{BiopetExecutable, MainCommand}
 
 object BiopetExecutablePublic extends BiopetExecutable {
   def publicPipelines: List[MainCommand] = List(

public/biopet-tools-package/pom.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <parent>
+        <artifactId>Biopet</artifactId>
+        <groupId>nl.lumc.sasc</groupId>
+        <version>0.5.0-SNAPSHOT</version>
+    </parent>
+    <modelVersion>4.0.0</modelVersion>
+
+    <artifactId>BiopetToolsPackage</artifactId>
+
+    <properties>
+        <sting.shade.phase>package</sting.shade.phase>
+        <app.main.class>nl.lumc.sasc.biopet.BiopetToolsExecutable</app.main.class>
+    </properties>
+
+    <dependencies>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>BiopetTools</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+    </dependencies>
+
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-shade-plugin</artifactId>
+                <version>2.4.1</version>
+                <configuration>
+                    <!--suppress MavenModelInspection -->
+                    <finalName>BiopetTools-${project.version}-${git.commit.id.abbrev}</finalName>
+                    <transformers>
+                        <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+                            <manifestEntries>
+                                <Main-Class>${app.main.class}</Main-Class>
+                                <!--suppress MavenModelInspection -->
+                                <X-Compile-Source-JDK>${maven.compile.source}</X-Compile-Source-JDK>
+                                <!--suppress MavenModelInspection -->
+                                <X-Compile-Target-JDK>${maven.compile.target}</X-Compile-Target-JDK>
+                            </manifestEntries>
+                        </transformer>
+                    </transformers>
+                    <filters>
+                    </filters>
+                </configuration>
+                <executions>
+                    <execution>
+                        <phase>package</phase>
+                        <goals>
+                            <goal>shade</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build>
+</project>
\ No newline at end of file

public/biopet-tools-package/src/main/scala/nl/lumc/sasc/biopet/BiopetToolsExecutable.scala

+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * 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
+
+import nl.lumc.sasc.biopet.utils.{ BiopetExecutable, MainCommand }
+
+object BiopetToolsExecutable extends BiopetExecutable {
+
+  def pipelines: List[MainCommand] = Nil
+
+  def tools: List[MainCommand] = List(
+    nl.lumc.sasc.biopet.tools.MergeTables,
+    nl.lumc.sasc.biopet.tools.WipeReads,
+    nl.lumc.sasc.biopet.tools.ExtractAlignedFastq,
+    nl.lumc.sasc.biopet.tools.FastqSync,
+    nl.lumc.sasc.biopet.tools.BiopetFlagstat,
+    nl.lumc.sasc.biopet.tools.CheckAllelesVcfInBam,
+    nl.lumc.sasc.biopet.tools.VcfToTsv,
+    nl.lumc.sasc.biopet.tools.VcfFilter,
+    nl.lumc.sasc.biopet.tools.VcfStats,
+    nl.lumc.sasc.biopet.tools.FindRepeatsPacBio,
+    nl.lumc.sasc.biopet.tools.MpileupToVcf,
+    nl.lumc.sasc.biopet.tools.FastqSplitter,
+    nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts,
+    nl.lumc.sasc.biopet.tools.SageCountFastq,
+    nl.lumc.sasc.biopet.tools.SageCreateLibrary,
+    nl.lumc.sasc.biopet.tools.SageCreateTagCounts,
+    nl.lumc.sasc.biopet.tools.BastyGenerateFasta,
+    nl.lumc.sasc.biopet.tools.MergeAlleles,
+    nl.lumc.sasc.biopet.tools.SamplesTsvToJson,
+    nl.lumc.sasc.biopet.tools.SeqStat,
+    nl.lumc.sasc.biopet.tools.VepNormalizer,
+    nl.lumc.sasc.biopet.tools.AnnotateVcfWithBed,
+    nl.lumc.sasc.biopet.tools.VcfWithVcf)
+}

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala

@@ -20,6 +20,7 @@ import java.io.File
 import htsjdk.variant.variantcontext.VariantContextBuilder
 import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
 import htsjdk.variant.vcf.{ VCFFileReader, VCFHeaderLineCount, VCFHeaderLineType, VCFInfoHeaderLine }
+import nl.lumc.sasc.biopet.utils.ToolCommand
 import nl.lumc.sasc.biopet.utils.intervals.{ BedRecord, BedRecordList }
 
 import scala.collection.JavaConversions._

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala

@@ -21,6 +21,7 @@ import htsjdk.samtools.SamReaderFactory
 import htsjdk.samtools.reference.IndexedFastaSequenceFile
 import htsjdk.variant.variantcontext.VariantContext
 import htsjdk.variant.vcf.VCFFileReader
+import nl.lumc.sasc.biopet.utils.ToolCommand
 import nl.lumc.sasc.biopet.utils.VcfUtils._
 
 import scala.collection.JavaConversions._

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala

@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.tools
 import java.io.{ File, PrintWriter }
 
 import htsjdk.samtools.{ SAMSequenceRecord, SamReaderFactory }
+import nl.lumc.sasc.biopet.utils.ToolCommand
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
 import scala.io.Source

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala

@@ -17,6 +17,8 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.{ File, PrintWriter }
 
+import nl.lumc.sasc.biopet.utils.ToolCommand
+
 import scala.collection.{ SortedMap, mutable }
 import scala.io.Source
 

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.tools
 import java.io.{ File, PrintWriter }
 
 import htsjdk.samtools.{ SAMRecord, SamReaderFactory }
-import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.utils.{ ToolCommand, ConfigUtils }
 
 import scala.collection.JavaConversions._
 import scala.collection.mutable

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala

@@ -21,6 +21,7 @@ import htsjdk.samtools.{ QueryInterval, SAMRecord, SamReader, SamReaderFactory }
 import htsjdk.variant.variantcontext.{ VariantContext, VariantContextBuilder }
 import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
 import htsjdk.variant.vcf.{ VCFFileReader, VCFHeaderLineCount, VCFHeaderLineType, VCFInfoHeaderLine }
+import nl.lumc.sasc.biopet.utils.ToolCommand
 
 import scala.collection.JavaConversions._
 import scala.collection.mutable

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala

@@ -20,6 +20,7 @@ import java.io.File
 import htsjdk.samtools.{ QueryInterval, SamReaderFactory, ValidationStringency }
 import htsjdk.samtools.fastq.{ BasicFastqWriter, FastqReader, FastqRecord }
 import htsjdk.samtools.util.Interval
+import nl.lumc.sasc.biopet.utils.ToolCommand
 
 import scala.collection.JavaConverters._
 import scala.collection.mutable.{ Set => MSet }

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala

@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.tools
 import java.io.File
 
 import htsjdk.samtools.fastq.{ AsyncFastqWriter, BasicFastqWriter, FastqReader }
+import nl.lumc.sasc.biopet.utils.ToolCommand
 
 object FastqSplitter extends ToolCommand {
 

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala

@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.tools
 import java.io.File
 
 import htsjdk.samtools.fastq.{ AsyncFastqWriter, BasicFastqWriter, FastqReader, FastqRecord }
+import nl.lumc.sasc.biopet.utils.ToolCommand
 
 import scala.annotation.tailrec
 import scala.collection.JavaConverters._

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala

@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.tools
 import java.io.{ PrintWriter, File }
 
 import htsjdk.samtools.{ QueryInterval, SAMRecord, SamReaderFactory, ValidationStringency }
+import nl.lumc.sasc.biopet.utils.ToolCommand
 
 import scala.collection.JavaConversions._
 import scala.io.Source

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala

@@ -21,6 +21,7 @@ import htsjdk.samtools.reference.FastaSequenceFile
 import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
 import htsjdk.variant.variantcontext.{ Allele, VariantContext, VariantContextBuilder }
 import htsjdk.variant.vcf.{ VCFFileReader, VCFHeader }
+import nl.lumc.sasc.biopet.utils.ToolCommand
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
 import scala.collection.JavaConversions._

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala

@@ -17,6 +17,8 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.{ BufferedWriter, File, FileWriter, OutputStreamWriter }
 
+import nl.lumc.sasc.biopet.utils.ToolCommand
+
 import scala.collection.mutable.{ Set => MutSet }
 import scala.io.{ BufferedSource, Source }
 

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala

@@ -17,6 +17,8 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.{ File, PrintWriter }
 
+import nl.lumc.sasc.biopet.utils.ToolCommand
+
 import scala.collection.mutable
 import scala.collection.mutable.ArrayBuffer
 import scala.io.Source

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala

@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.tools
 import java.io.File
 
 import htsjdk.samtools.fastq.{ AsyncFastqWriter, BasicFastqWriter, FastqReader, FastqRecord }
+import nl.lumc.sasc.biopet.utils.ToolCommand
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
 object PrefixFastq extends ToolCommand {

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala

@@ -19,6 +19,7 @@ import java.io.{ PrintWriter, InputStream, File }
 import java.util
 
 import htsjdk.variant.vcf.VCFFileReader
+import nl.lumc.sasc.biopet.utils.ToolCommand
 import nl.lumc.sasc.biopet.utils.rscript.ScatterPlot
 import nl.lumc.sasc.biopet.utils.intervals.{ BedRecord, BedRecordList }
 

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala

@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.{ File, FileReader, PrintWriter }
 
+import nl.lumc.sasc.biopet.utils.ToolCommand
 import org.biojava3.sequencing.io.fastq.{ Fastq, StreamListener, SangerFastqReader }
 
 import scala.collection.{ SortedMap, mutable }

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala

@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.{ File, PrintWriter }
 
+import nl.lumc.sasc.biopet.utils.ToolCommand
 import org.biojava3.core.sequence.DNASequence
 import org.biojava3.core.sequence.io.FastaReaderHelper
 

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala

@@ -17,6 +17,8 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.{ File, PrintWriter }
 
+import nl.lumc.sasc.biopet.utils.ToolCommand
+
 import scala.collection.{ SortedMap, mutable }
 import scala.io.Source
 

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala

@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.tools
 import java.io.{ PrintWriter, File }
 
 import nl.lumc.sasc.biopet.utils.ConfigUtils._
+import nl.lumc.sasc.biopet.utils.ToolCommand
 import scala.collection.mutable
 
 import scala.io.Source

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.tools
 import java.io.{ PrintWriter, File }
 
 import htsjdk.samtools.fastq.{ FastqReader, FastqRecord }
-import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.utils.{ ToolCommand, ConfigUtils }
 
 import scala.collection.JavaConverters._
 import scala.collection.immutable.Map

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala

@@ -2,6 +2,7 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.File
 
+import nl.lumc.sasc.biopet.utils.ToolCommand
 import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
 
 /**

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala

@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.{ PrintWriter, File }
 
+import nl.lumc.sasc.biopet.utils.ToolCommand
 import nl.lumc.sasc.biopet.utils.summary.Summary
 
 /**

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala

@@ -20,6 +20,7 @@ import java.io.File
 import htsjdk.variant.variantcontext.{ GenotypeType, VariantContext }
 import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
 import htsjdk.variant.vcf.VCFFileReader
+import nl.lumc.sasc.biopet.utils.ToolCommand
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
 import scala.collection.JavaConversions._

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala

@@ -21,6 +21,7 @@ import htsjdk.samtools.reference.FastaSequenceFile
 import htsjdk.samtools.util.Interval
 import htsjdk.variant.variantcontext.{ Allele, Genotype, VariantContext }
 import htsjdk.variant.vcf.VCFFileReader
+import nl.lumc.sasc.biopet.utils.ToolCommand
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
 

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala

@@ -19,6 +19,7 @@ import java.io.{ File, PrintStream }
 import java.text.DecimalFormat
 
 import htsjdk.variant.vcf.VCFFileReader
+import nl.lumc.sasc.biopet.utils.ToolCommand
 
 import scala.collection.JavaConversions._
 import scala.collection.mutable

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala

@@ -21,6 +21,7 @@ import java.util
 import htsjdk.variant.variantcontext.{ VariantContext, VariantContextBuilder }
 import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
 import htsjdk.variant.vcf._
+import nl.lumc.sasc.biopet.utils.ToolCommand
 import nl.lumc.sasc.biopet.utils.VcfUtils.scalaListToJavaObjectArrayList
 
 import scala.collection.JavaConversions._

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala

@@ -21,6 +21,7 @@ import htsjdk.tribble.TribbleException
 import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
 import htsjdk.variant.variantcontext.{ VariantContext, VariantContextBuilder }
 import htsjdk.variant.vcf._
+import nl.lumc.sasc.biopet.utils.ToolCommand
 
 import scala.collection.JavaConversions._
 import scala.collection.mutable.{ Map => MMap }

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala

@@ -20,6 +20,7 @@ import java.io.File
 import com.google.common.hash.{ PrimitiveSink, Funnel, BloomFilter }
 import htsjdk.samtools.{ QueryInterval, SAMFileWriter, SAMFileWriterFactory, SAMRecord, SamReader, SamReaderFactory, ValidationStringency }
 import htsjdk.samtools.util.{ Interval, IntervalTreeMap }
+import nl.lumc.sasc.biopet.utils.ToolCommand
 import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
 import org.apache.commons.io.FilenameUtils.getExtension
 

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala → public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BiopetExecutable.scala

@@ -13,12 +13,10 @@
  * 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.core
+package nl.lumc.sasc.biopet.utils
 
 import java.io.{ PrintWriter, StringWriter }
 
-import nl.lumc.sasc.biopet.core.BiopetExecutable._
-import nl.lumc.sasc.biopet.utils.{ MainCommand, Logging }
 import nl.lumc.sasc.biopet.{ FullVersion, LastCommitHash }
 import org.apache.log4j.Logger
 
@@ -89,7 +87,7 @@ trait BiopetExecutable extends Logging {
       case Array("version") =>
         println("version: " + FullVersion)
       case Array("license") =>
-        println(getLicense)
+        println(BiopetExecutable.getLicense)
       case Array(module, name, passArgs @ _*) =>
         try {
           getCommand(module, name).main(passArgs.toArray)

public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/tools/ToolCommand.scala → public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ToolCommand.scala

@@ -13,9 +13,8 @@
  * 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.tools
+package nl.lumc.sasc.biopet.utils
 
-import nl.lumc.sasc.biopet.utils.{ Logging, MainCommand }
 import nl.lumc.sasc.biopet.FullVersion
 
 /**

public/pom.xml

@@ -45,6 +45,7 @@
         <module>biopet-tools</module>
         <module>biopet-tools-extensions</module>
         <module>biopet-extentsions</module>
+        <module>biopet-tools-package</module>
     </modules>
 
     <properties>