基因数据处理36之qc-metrics安装

更多代码请见：https://github.com/xubo245/SparkLearning
Spark中组件Mllib的学习之基础概念篇
1解释
Read and variant metrics,useable for pipeline quality control purposes
qc-metrics主要是用于read和变异的度量，流水线质量控制的目的

2.代码：

git clone  https://github.com/xubo245/qc-metrics.git
cd qc-metrics/
mvn clean package -DskipTests

3.结果：

xubo@xubo:~/xubo/tools/qc-metrics$ mvn clean package -DskipTests
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] qc-metrics
[INFO] QC Metrics: Core
[INFO] QC Metrics: CLI
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building qc-metrics 0.0.2-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.6.1:clean (default-clean) @ qc-metrics-parent_2.10 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ qc-metrics-parent_2.10 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ qc-metrics-parent_2.10 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ qc-metrics-parent_2.10 ---
[INFO] Modified 0 of 18 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ qc-metrics-parent_2.10 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ qc-metrics-parent_2.10 ---
[INFO] No sources to compile
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building QC Metrics: Core 0.0.2-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading: https://repo.maven.apache.org/maven2/org/apache/avro/avro/1.7.4/avro-1.7.4.pom
Downloaded: https://repo.maven.apache.org/maven2/org/apache/avro/avro/1.7.4/avro-1.7.4.pom (5 KB at 1.4 KB/sec)
Downloading: https://repo.maven.apache.org/maven2/org/apache/avro/avro-parent/1.7.4/avro-parent-1.7.4.pom
Downloaded: https://repo.maven.apache.org/maven2/org/apache/avro/avro-parent/1.7.4/avro-parent-1.7.4.pom (16 KB at 5.9 KB/sec)
Downloading: https://repo.maven.apache.org/maven2/org/apache/avro/avro-toplevel/1.7.4/avro-toplevel-1.7.4.pom
Downloaded: https://repo.maven.apache.org/maven2/org/apache/avro/avro-toplevel/1.7.4/avro-toplevel-1.7.4.pom (10 KB at 11.6 KB/sec)
Downloading: https://repo.maven.apache.org/maven2/org/xerial/snappy/snappy-java/1.0.4.1/snappy-java-1.0.4.1.pom
Downloaded: https://repo.maven.apache.org/maven2/org/xerial/snappy/snappy-java/1.0.4.1/snappy-java-1.0.4.1.pom (10 KB at 10.7 KB/sec)
Downloading: https://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-core_2.10/0.18.2/adam-core_2.10-0.18.2-tests.jar
Downloaded: https://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-core_2.10/0.18.2/adam-core_2.10-0.18.2-tests.jar (1565 KB at 46.6 KB/sec)
[INFO] 
[INFO] --- maven-clean-plugin:2.6.1:clean (default-clean) @ qc-metrics-core_2.10 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ qc-metrics-core_2.10 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ qc-metrics-core_2.10 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.9.1:add-source (add-source) @ qc-metrics-core_2.10 ---
[INFO] Source directory: /home/xubo/xubo/tools/qc-metrics/qc-metrics-core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ qc-metrics-core_2.10 ---
[INFO] Modified 0 of 13 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.7:resources (default-resources) @ qc-metrics-core_2.10 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/xubo/xubo/tools/qc-metrics/qc-metrics-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ qc-metrics-core_2.10 ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  com.twitter:chill_2.10:0.5.0 requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-remote_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-actor_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-slf4j_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.apache.spark:spark-core_2.10:1.4.1 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-jackson_2.10:3.2.10 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-core_2.10:3.2.10 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-ast_2.10:3.2.10 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-core_2.10:3.2.10 requires scala version: 2.10.0
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/xubo/xubo/tools/qc-metrics/qc-metrics-core/src/main/scala:-1: info: compiling
[INFO] Compiling 8 source files to /home/xubo/xubo/tools/qc-metrics/qc-metrics-core/target/scala-2.10.4/classes at 1464499989517
[WARNING] warning: there were 2 feature warning(s); re-run with -feature for details
[WARNING] one warning found
[INFO] prepare-compile in 0 s
[INFO] compile in 32 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ qc-metrics-core_2.10 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.9.1:add-test-source (add-test-source) @ qc-metrics-core_2.10 ---
[INFO] Test Source directory: /home/xubo/xubo/tools/qc-metrics/qc-metrics-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:2.7:testResources (default-testResources) @ qc-metrics-core_2.10 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ qc-metrics-core_2.10 ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  com.twitter:chill_2.10:0.5.0 requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-remote_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-actor_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-slf4j_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.apache.spark:spark-core_2.10:1.4.1 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-jackson_2.10:3.2.10 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-core_2.10:3.2.10 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-ast_2.10:3.2.10 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-core_2.10:3.2.10 requires scala version: 2.10.0
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/xubo/xubo/tools/qc-metrics/qc-metrics-core/src/test/scala:-1: info: compiling
[INFO] Compiling 5 source files to /home/xubo/xubo/tools/qc-metrics/qc-metrics-core/target/scala-2.10.4/test-classes at 1464500025815
[INFO] prepare-compile in 0 s
[INFO] compile in 25 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ qc-metrics-core_2.10 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.18.1:test (default-test) @ qc-metrics-core_2.10 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ qc-metrics-core_2.10 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:2.6:jar (default-jar) @ qc-metrics-core_2.10 ---
[INFO] Building jar: /home/xubo/xubo/tools/qc-metrics/qc-metrics-core/target/qc-metrics-core_2.10-0.0.2-SNAPSHOT.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building QC Metrics: CLI 0.0.2-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.6.1:clean (default-clean) @ qc-metrics-cli_2.10 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ qc-metrics-cli_2.10 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ qc-metrics-cli_2.10 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.9.1:add-source (add-source) @ qc-metrics-cli_2.10 ---
[INFO] Source directory: /home/xubo/xubo/tools/qc-metrics/qc-metrics-cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ qc-metrics-cli_2.10 ---
[INFO] Modified 0 of 5 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.7:resources (default-resources) @ qc-metrics-cli_2.10 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/xubo/xubo/tools/qc-metrics/qc-metrics-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ qc-metrics-cli_2.10 ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:1.1.1 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.18.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.qc-metrics:qc-metrics-core_2.10:0.0.2-SNAPSHOT requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.3 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-io_2.10:0.2.3 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-apis_2.10:0.18.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-cli_2.10:0.18.2 requires scala version: 2.10.4
[WARNING]  net.codingwell:scala-guice_2.10:4.0.0 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.18.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.3 requires scala version: 2.10.4
[WARNING]  org.scalatest:scalatest_2.10:2.2.5 requires scala version: 2.10.4
[WARNING]  org.scala-lang:scala-reflect:2.10.5 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.10:0.2.3 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.10:0.2.3 requires scala version: 2.10.4
[WARNING]  com.twitter:chill_2.10:0.5.0 requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-remote_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-actor_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-slf4j_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.apache.spark:spark-core_2.10:1.4.1 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-jackson_2.10:3.2.10 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-core_2.10:3.2.10 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-ast_2.10:3.2.10 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-core_2.10:3.2.10 requires scala version: 2.10.0
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/xubo/xubo/tools/qc-metrics/qc-metrics-cli/src/main/scala:-1: info: compiling
[INFO] Compiling 5 source files to /home/xubo/xubo/tools/qc-metrics/qc-metrics-cli/target/scala-2.10.4/classes at 1464500054463
[INFO] prepare-compile in 0 s
[INFO] compile in 17 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ qc-metrics-cli_2.10 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.9.1:add-test-source (add-test-source) @ qc-metrics-cli_2.10 ---
[INFO] Test Source directory: /home/xubo/xubo/tools/qc-metrics/qc-metrics-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:2.7:testResources (default-testResources) @ qc-metrics-cli_2.10 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/xubo/xubo/tools/qc-metrics/qc-metrics-cli/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ qc-metrics-cli_2.10 ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:1.1.1 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.18.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.qc-metrics:qc-metrics-core_2.10:0.0.2-SNAPSHOT requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.3 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-io_2.10:0.2.3 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-apis_2.10:0.18.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-cli_2.10:0.18.2 requires scala version: 2.10.4
[WARNING]  net.codingwell:scala-guice_2.10:4.0.0 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.18.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.3 requires scala version: 2.10.4
[WARNING]  org.scalatest:scalatest_2.10:2.2.5 requires scala version: 2.10.4
[WARNING]  org.scala-lang:scala-reflect:2.10.5 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.10:0.2.3 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.10:0.2.3 requires scala version: 2.10.4
[WARNING]  com.twitter:chill_2.10:0.5.0 requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-remote_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-actor_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-slf4j_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.apache.spark:spark-core_2.10:1.4.1 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-jackson_2.10:3.2.10 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-core_2.10:3.2.10 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-ast_2.10:3.2.10 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-core_2.10:3.2.10 requires scala version: 2.10.0
[WARNING] Multiple versions of scala libraries detected!
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ qc-metrics-cli_2.10 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.18.1:test (default-test) @ qc-metrics-cli_2.10 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ qc-metrics-cli_2.10 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:2.6:jar (default-jar) @ qc-metrics-cli_2.10 ---
[INFO] Building jar: /home/xubo/xubo/tools/qc-metrics/qc-metrics-cli/target/qc-metrics-cli_2.10-0.0.2-SNAPSHOT.jar
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] qc-metrics ......................................... SUCCESS [  4.986 s]
[INFO] QC Metrics: Core ................................... SUCCESS [01:53 min]
[INFO] QC Metrics: CLI .................................... SUCCESS [ 19.544 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 02:18 min
[INFO] Finished at: 2016-05-29T13:34:31+08:00
[INFO] Final Memory: 29M/357M
[INFO] ------------------------------------------------------------------------

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