Commit 394f32a2 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed compile errors

parent 45fce26a
......@@ -2,22 +2,22 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.Output
/**
* Created by pjvan_thof on 8/11/15.
*/
class Curl(val root: Configurable) extends BiopetCommandLineFunction {
class Curl(val root: Configurable) extends BiopetCommandLineFunction with Version {
@Output
var output: File = _
var url: String = _
executable = config("exe", default = "curl")
override def versionCommand = executable + " --version"
override def versionRegex = """curl (\w+\.\w+\.\w+) .*""".r
def versionCommand = executable + " --version"
def versionRegex = """curl (\w+\.\w+\.\w+) .*""".r
def cmdLine: String = required(executable) + required(url) + " > " + required(output)
}
......@@ -2,14 +2,14 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Argument, Input}
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input }
/**
* Created by pjvan_thof on 8/11/15.
*/
class TarExtract(val root: Configurable) extends BiopetCommandLineFunction {
class TarExtract(val root: Configurable) extends BiopetCommandLineFunction with Version {
@Input(required = true)
var inputTar: File = _
......@@ -17,8 +17,8 @@ class TarExtract(val root: Configurable) extends BiopetCommandLineFunction {
var outputDir: File = _
executable = config("exe", default = "tar", freeVar = false)
override def versionCommand = executable + " --version"
override def versionRegex = """tar \(GNU tar\) (.*)""".r
def versionCommand = executable + " --version"
def versionRegex = """tar \(GNU tar\) (.*)""".r
override def beforeGraph: Unit = {
super.beforeGraph
......
......@@ -13,7 +13,7 @@
* 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
package nl.lumc.sasc.biopet.extensions.bowtie
import java.io.File
......
......@@ -2,14 +2,14 @@ package nl.lumc.sasc.biopet.extensions.bowtie
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Argument, Input}
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input }
/**
* Created by pjvan_thof on 8/15/15.
*/
class Bowtie2Build(val root: Configurable) extends BiopetCommandLineFunction {
class Bowtie2Build(val root: Configurable) extends BiopetCommandLineFunction with Version {
@Input(required = true)
var reference: File = _
......@@ -17,8 +17,8 @@ class Bowtie2Build(val root: Configurable) extends BiopetCommandLineFunction {
var baseName: String = _
executable = config("exe", default = "bowtie2-build", freeVar = false)
override def versionRegex = """.*[Vv]ersion:? (\d*\.\d*\.\d*)""".r
override def versionCommand = executable + " --version"
def versionRegex = """.*[Vv]ersion:? (\d*\.\d*\.\d*)""".r
def versionCommand = executable + " --version"
override def defaultCoreMemory = 15.0
......
......@@ -2,14 +2,14 @@ package nl.lumc.sasc.biopet.extensions.bowtie
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Argument, Input}
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input }
/**
* Created by pjvan_thof on 8/15/15.
*/
class BowtieBuild(val root: Configurable) extends BiopetCommandLineFunction {
class BowtieBuild(val root: Configurable) extends BiopetCommandLineFunction with Version {
@Input(required = true)
var reference: File = _
......@@ -17,8 +17,8 @@ class BowtieBuild(val root: Configurable) extends BiopetCommandLineFunction {
var baseName: String = _
executable = config("exe", default = "bowtie-build", freeVar = false)
override def versionRegex = """.*[Vv]ersion:? (\d*\.\d*\.\d*)""".r
override def versionCommand = executable + " --version"
def versionRegex = """.*[Vv]ersion:? (\d*\.\d*\.\d*)""".r
def versionCommand = executable + " --version"
override def defaultCoreMemory = 15.0
......
......@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.bwa
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Extension for bwa aln
......
......@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.gmap
import java.io.File
import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Reference}
import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction, Reference }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.Input
......@@ -25,7 +25,7 @@ import org.broadinstitute.gatk.utils.commandline.Input
* Wrapper for the gsnap command line tool
* Written based on gsnap version 2014-05-15
*/
class GmapBuild(val root: Configurable) extends BiopetCommandLineFunction with Reference {
class GmapBuild(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
/** default executable */
executable = config("exe", default = "gmap_build", freeVar = false)
......@@ -42,8 +42,8 @@ class GmapBuild(val root: Configurable) extends BiopetCommandLineFunction with R
override def defaultCoreMemory = 25.0
override def versionRegex = """.* version (.*)""".r
override def versionCommand = executable
def versionRegex = """.* version (.*)""".r
def versionCommand = executable
override def versionExitcode = List(0, 1, 255)
override def beforeGraph: Unit = {
......
......@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class CreateSequenceDictionary(val root: Configurable) extends Picard {
......
......@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.samtools
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Extension for samtools flagstat */
class SamtoolsFaidx(val root: Configurable) extends Samtools {
......
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