bigdatagenomics / pacmin Goto Github PK

Builds on #1 and #7.

http://derecho.elijah.cs.cmu.edu:8585/bigdatagenomics

Instead, we should rely on the MinHashing implementation which is in bigdatagenomics/utils#2. They're actually the same; we've just moved where it'll sit, since it isn't genomics specific code.

I have been trying to build this package using maven however it has no success yet. Could you give some direction please?

These are the info during my build from the github source

$ mvn -X clean package -DskipTests
$ mvn -version
Apache Maven 3.3.9 (bb52d8502b132ec0a5a3f4c09453c07478323dc5; 2015-11-10T17:41:47+01:00)
Maven home: /usr/share/maven3
Java version: 1.7.0_80, vendor: Oracle Corporation
Java home: /usr/lib/jvm/java-7-oracle/jre
Default locale: en_US, platform encoding: UTF-8
OS name: "linux", version: "4.2.0-42-generic", arch: "amd64", family: "unix"

These are the error message:

[ERROR] Failed to execute goal net.alchim31.maven:scala-maven-plugin:3.1.5:compile (scala-compile-first) on project pacmin-core: Execution scala-compile-first of goal net.alchim31.maven:scala-maven-plugin:3.1.5:compile failed. CompileFailed -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal net.alchim31.maven:scala-maven-plugin:3.1.5:compile (scala-compile-first) on project pacmin-core: Execution scala-compile-first of goal net.alchim31.maven:scala-maven-plugin:3.1.5:compile failed.
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:212)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:116)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:80)
at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51)
at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:307)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:193)
at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:106)
at org.apache.maven.cli.MavenCli.execute(MavenCli.java:863)
at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:288)
at org.apache.maven.cli.MavenCli.main(MavenCli.java:199)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
Caused by: org.apache.maven.plugin.PluginExecutionException: Execution scala-compile-first of goal net.alchim31.maven:scala-maven-plugin:3.1.5:compile failed.
at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:145)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:207)
... 20 more
Caused by: Compile failed via zinc server
at sbt_inc.SbtIncrementalCompiler.zincCompile(SbtIncrementalCompiler.java:119)
at sbt_inc.SbtIncrementalCompiler.compile(SbtIncrementalCompiler.java:71)
at scala_maven.ScalaCompilerSupport.incrementalCompile(ScalaCompilerSupport.java:296)
at scala_maven.ScalaCompilerSupport.compile(ScalaCompilerSupport.java:123)
at scala_maven.ScalaCompilerSupport.doExecute(ScalaCompilerSupport.java:104)
at scala_maven.ScalaMojoSupport.execute(ScalaMojoSupport.java:460)
at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:134)
... 21 more
[ERROR]
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/PluginExecutionException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR] mvn -rf :pacmin-core

#8 moved to using Jaccard similarity to approximate overlap length. Instead, we can use an indexed de Bruijn graph to resolve the approximate overlap length.

The current overlap graph has the edges and vertices swapped.

Additionally, we'll store alignments as range equivalences.