基因数据处理55之cs-bwamem安装记录（idea maven ，没有通过pl）

project下的pom

    D:\1win7\java\jdk\bin\java "-Dmaven.home=D:\1win7\idea\IntelliJ IDEA Community Edition 15.0.4\plugins\maven\lib\maven3" "-Dclassworlds.conf=D:\1win7\idea\IntelliJ IDEA Community Edition 15.0.4\plugins\maven\lib\maven3\bin\m2.conf" -Didea.launcher.port=7535 "-Didea.launcher.bin.path=D:\1win7\idea\IntelliJ IDEA Community Edition 15.0.4\bin" -Dfile.encoding=UTF-8 -classpath "D:\1win7\idea\IntelliJ IDEA Community Edition 15.0.4\plugins\maven\lib\maven3\boot\plexus-classworlds-2.4.jar;D:\1win7\idea\IntelliJ IDEA Community Edition 15.0.4\lib\idea_rt.jar" com.intellij.rt.execution.application.AppMain org.codehaus.classworlds.Launcher -Didea.version=15.0.4 compile    [INFO] Scanning for projects...    [WARNING]     [WARNING] Some problems were encountered while building the effective model for cs.ucla.edu:cloud-scale-bwamem:jar:0.2.0    [WARNING] 'dependencies.dependency.systemPath' for org.apache.spark:spark-core_${scala.artifact.suffix}:jar should use a variable instead of a hard-coded path D:/1win7/java/otherJar/spark-assembly-1.5.2-hadoop2.6.0.jar @ line 246, column 25    [WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-shade-plugin is missing. @ line 145, column 21    [WARNING] 'build.plugins.plugin.version' for org.scala-tools:maven-scala-plugin is missing. @ line 89, column 21    [WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 227, column 29    [WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 231, column 29    [WARNING]     [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.    [WARNING]     [WARNING] For this reason, future Maven versions might no longer support building such malformed projects.    [WARNING]     [INFO]                                                                             [INFO] ------------------------------------------------------------------------    [INFO] Building Cloud-Scale-BWAMEM 0.2.0    [INFO] ------------------------------------------------------------------------    Downloading: http://scala-tools.org/repo-releases/org/scala-tools/maven-scala-plugin/maven-metadata.xml    Downloading: http://scala-tools.org/repo-releases/org/apache/maven/plugins/maven-shade-plugin/maven-metadata.xml    Downloading: http://repo.akka.io/releases/com/twitter/parquet-column/1.4.3/parquet-column-1.4.3.pom    Downloading: http://scala-tools.org/repo-releases/com/twitter/parquet-column/1.4.3/parquet-column-1.4.3.pom    [WARNING] The POM for com.twitter:parquet-column:jar:1.4.3 is missing, no dependency information available    Downloading: http://repo.akka.io/releases/com/twitter/parquet-hadoop/1.4.3/parquet-hadoop-1.4.3.pom    Downloading: http://scala-tools.org/repo-releases/com/twitter/parquet-hadoop/1.4.3/parquet-hadoop-1.4.3.pom    Downloading: http://repo1.maven.org/maven2/com/twitter/parquet-hadoop/1.4.3/parquet-hadoop-1.4.3.pom    Downloaded: http://repo1.maven.org/maven2/com/twitter/parquet-hadoop/1.4.3/parquet-hadoop-1.4.3.pom (4 KB at 4.5 KB/sec)    Downloading: http://repo.akka.io/releases/com/twitter/parquet-format/2.0.0/parquet-format-2.0.0.pom    Downloading: http://scala-tools.org/repo-releases/com/twitter/parquet-format/2.0.0/parquet-format-2.0.0.pom    Downloading: http://repo1.maven.org/maven2/com/twitter/parquet-format/2.0.0/parquet-format-2.0.0.pom    Downloaded: http://repo1.maven.org/maven2/com/twitter/parquet-format/2.0.0/parquet-format-2.0.0.pom (6 KB at 11.6 KB/sec)    Downloading: http://repo.akka.io/releases/com/twitter/parquet-jackson/1.4.3/parquet-jackson-1.4.3.pom    Downloading: http://scala-tools.org/repo-releases/com/twitter/parquet-jackson/1.4.3/parquet-jackson-1.4.3.pom    Downloading: http://repo1.maven.org/maven2/com/twitter/parquet-jackson/1.4.3/parquet-jackson-1.4.3.pom    Downloaded: http://repo1.maven.org/maven2/com/twitter/parquet-jackson/1.4.3/parquet-jackson-1.4.3.pom (3 KB at 5.7 KB/sec)    Downloading: http://repo.akka.io/releases/org/bdgenomics/bdg-formats/bdg-formats/0.2.0/bdg-formats-0.2.0.pom    Downloading: http://scala-tools.org/repo-releases/org/bdgenomics/bdg-formats/bdg-formats/0.2.0/bdg-formats-0.2.0.pom    Downloading: http://repo1.maven.org/maven2/org/bdgenomics/bdg-formats/bdg-formats/0.2.0/bdg-formats-0.2.0.pom    Downloaded: http://repo1.maven.org/maven2/org/bdgenomics/bdg-formats/bdg-formats/0.2.0/bdg-formats-0.2.0.pom (5 KB at 7.9 KB/sec)    Downloading: http://repo.akka.io/releases/org/bdgenomics/adam/adam-core/0.14.0/adam-core-0.14.0.pom    Downloading: http://scala-tools.org/repo-releases/org/bdgenomics/adam/adam-core/0.14.0/adam-core-0.14.0.pom    Downloading: http://repo1.maven.org/maven2/org/bdgenomics/adam/adam-core/0.14.0/adam-core-0.14.0.pom    Downloaded: http://repo1.maven.org/maven2/org/bdgenomics/adam/adam-core/0.14.0/adam-core-0.14.0.pom (8 KB at 11.6 KB/sec)    Downloading: http://repo.akka.io/releases/org/bdgenomics/adam/adam-parent/0.14.0/adam-parent-0.14.0.pom    Downloading: http://scala-tools.org/repo-releases/org/bdgenomics/adam/adam-parent/0.14.0/adam-parent-0.14.0.pom    Downloading: http://repo1.maven.org/maven2/org/bdgenomics/adam/adam-parent/0.14.0/adam-parent-0.14.0.pom    Downloaded: http://repo1.maven.org/maven2/org/bdgenomics/adam/adam-parent/0.14.0/adam-parent-0.14.0.pom (20 KB at 9.9 KB/sec)    Downloading: http://repo.akka.io/releases/org/scoverage/scalac-scoverage-plugin_2.10/0.99.2/scalac-scoverage-plugin_2.10-0.99.2.pom    Downloading: http://scala-tools.org/repo-releases/org/scoverage/scalac-scoverage-plugin_2.10/0.99.2/scalac-scoverage-plugin_2.10-0.99.2.pom    [WARNING] The POM for org.scoverage:scalac-scoverage-plugin_2.10:jar:0.99.2 is missing, no dependency information available    Downloading: http://repo.akka.io/releases/org/apache/spark/spark-core_2.10/1.1.0/spark-core_2.10-1.1.0.pom    Downloading: http://scala-tools.org/repo-releases/org/apache/spark/spark-core_2.10/1.1.0/spark-core_2.10-1.1.0.pom    Downloading: http://repo1.maven.org/maven2/org/apache/spark/spark-core_2.10/1.1.0/spark-core_2.10-1.1.0.pom    Downloaded: http://repo1.maven.org/maven2/org/apache/spark/spark-core_2.10/1.1.0/spark-core_2.10-1.1.0.pom (11 KB at 4.9 KB/sec)    Downloading: http://repo.akka.io/releases/org/apache/spark/spark-parent/1.1.0/spark-parent-1.1.0.pom    Downloading: http://scala-tools.org/repo-releases/org/apache/spark/spark-parent/1.1.0/spark-parent-1.1.0.pom    Downloading: http://repo1.maven.org/maven2/org/apache/spark/spark-parent/1.1.0/spark-parent-1.1.0.pom    Downloaded: http://repo1.maven.org/maven2/org/apache/spark/spark-parent/1.1.0/spark-parent-1.1.0.pom (40 KB at 26.4 KB/sec)    Downloading: http://repo.akka.io/releases/org/slf4j/jul-to-slf4j/1.7.5/jul-to-slf4j-1.7.5.pom    Downloading: http://scala-tools.org/repo-releases/org/slf4j/jul-to-slf4j/1.7.5/jul-to-slf4j-1.7.5.pom    [WARNING] The POM for org.slf4j:jul-to-slf4j:jar:1.7.5 is missing, no dependency information available    Downloading: http://repo.akka.io/releases/org/slf4j/jcl-over-slf4j/1.7.5/jcl-over-slf4j-1.7.5.pom    Downloading: http://scala-tools.org/repo-releases/org/slf4j/jcl-over-slf4j/1.7.5/jcl-over-slf4j-1.7.5.pom    [WARNING] The POM for org.slf4j:jcl-over-slf4j:jar:1.7.5 is missing, no dependency information available    Downloading: http://repo.akka.io/releases/com/ning/compress-lzf/1.0.0/compress-lzf-1.0.0.pom    Downloading: http://scala-tools.org/repo-releases/com/ning/compress-lzf/1.0.0/compress-lzf-1.0.0.pom    Downloading: http://repo1.maven.org/maven2/com/ning/compress-lzf/1.0.0/compress-lzf-1.0.0.pom    Downloaded: http://repo1.maven.org/maven2/com/ning/compress-lzf/1.0.0/compress-lzf-1.0.0.pom (8 KB at 14.1 KB/sec)    Downloading: http://repo.akka.io/releases/org/xerial/snappy/snappy-java/1.0.5.3/snappy-java-1.0.5.3.pom    Downloading: http://scala-tools.org/repo-releases/org/xerial/snappy/snappy-java/1.0.5.3/snappy-java-1.0.5.3.pom    Downloading: http://repo1.maven.org/maven2/org/xerial/snappy/snappy-java/1.0.5.3/snappy-java-1.0.5.3.pom    Downloaded: http://repo1.maven.org/maven2/org/xerial/snappy/snappy-java/1.0.5.3/snappy-java-1.0.5.3.pom (13 KB at 11.7 KB/sec)    Downloading: http://repo.akka.io/releases/com/twitter/chill_2.10/0.3.6/chill_2.10-0.3.6.pom    Downloading: http://scala-tools.org/repo-releases/com/twitter/chill_2.10/0.3.6/chill_2.10-0.3.6.pom    Downloading: http://repo1.maven.org/maven2/com/twitter/chill_2.10/0.3.6/chill_2.10-0.3.6.pom    Downloaded: http://repo1.maven.org/maven2/com/twitter/chill_2.10/0.3.6/chill_2.10-0.3.6.pom (3 KB at 4.8 KB/sec)    Downloading: http://repo.akka.io/releases/com/twitter/chill-java/0.3.6/chill-java-0.3.6.pom    Downloading: http://scala-tools.org/repo-releases/com/twitter/chill-java/0.3.6/chill-java-0.3.6.pom    Downloading: http://repo1.maven.org/maven2/com/twitter/chill-java/0.3.6/chill-java-0.3.6.pom    Downloaded: http://repo1.maven.org/maven2/com/twitter/chill-java/0.3.6/chill-java-0.3.6.pom (2 KB at 3.8 KB/sec)    Downloading: http://repo.akka.io/releases/org/spark-project/akka/akka-remote_2.10/2.2.3-shaded-protobuf/akka-remote_2.10-2.2.3-shaded-protobuf.pom    Downloading: http://scala-tools.org/repo-releases/org/spark-project/akka/akka-remote_2.10/2.2.3-shaded-protobuf/akka-remote_2.10-2.2.3-shaded-protobuf.pom    Downloading: http://repo1.maven.org/maven2/org/spark-project/akka/akka-remote_2.10/2.2.3-shaded-protobuf/akka-remote_2.10-2.2.3-shaded-protobuf.pom    Downloaded: http://repo1.maven.org/maven2/org/spark-project/akka/akka-remote_2.10/2.2.3-shaded-protobuf/akka-remote_2.10-2.2.3-shaded-protobuf.pom (4 KB at 7.1 KB/sec)    Downloading: http://repo.akka.io/releases/org/spark-project/akka/akka-actor_2.10/2.2.3-shaded-protobuf/akka-actor_2.10-2.2.3-shaded-protobuf.pom    Downloading: http://scala-tools.org/repo-releases/org/spark-project/akka/akka-actor_2.10/2.2.3-shaded-protobuf/akka-actor_2.10-2.2.3-shaded-protobuf.pom    Downloading: http://repo1.maven.org/maven2/org/spark-project/akka/akka-actor_2.10/2.2.3-shaded-protobuf/akka-actor_2.10-2.2.3-shaded-protobuf.pom    Downloaded: http://repo1.maven.org/maven2/org/spark-project/akka/akka-actor_2.10/2.2.3-shaded-protobuf/akka-actor_2.10-2.2.3-shaded-protobuf.pom (2 KB at 3.7 KB/sec)    Downloading: http://repo.akka.io/releases/com/typesafe/config/1.0.2/config-1.0.2.pom    [WARNING] The POM for com.typesafe:config:jar:1.0.2 is missing, no dependency information available    Downloading: http://repo.akka.io/releases/org/spark-project/protobuf/protobuf-java/2.4.1-shaded/protobuf-java-2.4.1-shaded.pom    [WARNING] The POM for org.spark-project.protobuf:protobuf-java:jar:2.4.1-shaded is missing, no dependency information available    Downloading: http://repo.akka.io/releases/org/spark-project/akka/akka-slf4j_2.10/2.2.3-shaded-protobuf/akka-slf4j_2.10-2.2.3-shaded-protobuf.pom    Downloading: http://scala-tools.org/repo-releases/org/spark-project/akka/akka-slf4j_2.10/2.2.3-shaded-protobuf/akka-slf4j_2.10-2.2.3-shaded-protobuf.pom    Downloading: http://repo1.maven.org/maven2/org/spark-project/akka/akka-slf4j_2.10/2.2.3-shaded-protobuf/akka-slf4j_2.10-2.2.3-shaded-protobuf.pom    Downloaded: http://repo1.maven.org/maven2/org/spark-project/akka/akka-slf4j_2.10/2.2.3-shaded-protobuf/akka-slf4j_2.10-2.2.3-shaded-protobuf.pom (3 KB at 4.7 KB/sec)    Downloading: http://repo.akka.io/releases/colt/colt/1.2.0/colt-1.2.0.pom    Downloading: http://scala-tools.org/repo-releases/colt/colt/1.2.0/colt-1.2.0.pom    [WARNING] The POM for colt:colt:jar:1.2.0 is missing, no dependency information available    Downloading: http://repo.akka.io/releases/org/apache/mesos/mesos/0.18.1/mesos-0.18.1.pom    Downloading: http://scala-tools.org/repo-releases/org/apache/mesos/mesos/0.18.1/mesos-0.18.1.pom    Downloading: http://repo1.maven.org/maven2/org/apache/mesos/mesos/0.18.1/mesos-0.18.1.pom    Downloaded: http://repo1.maven.org/maven2/org/apache/mesos/mesos/0.18.1/mesos-0.18.1.pom (8 KB at 9.8 KB/sec)    Downloading: http://repo.akka.io/releases/com/codahale/metrics/metrics-core/3.0.0/metrics-core-3.0.0.pom    Downloading: http://scala-tools.org/repo-releases/com/codahale/metrics/metrics-core/3.0.0/metrics-core-3.0.0.pom    Downloading: http://repo1.maven.org/maven2/com/codahale/metrics/metrics-core/3.0.0/metrics-core-3.0.0.pom    Downloaded: http://repo1.maven.org/maven2/com/codahale/metrics/metrics-core/3.0.0/metrics-core-3.0.0.pom (845 B at 1.6 KB/sec)    Downloading: http://repo.akka.io/releases/com/codahale/metrics/metrics-parent/3.0.0/metrics-parent-3.0.0.pom    Downloading: http://scala-tools.org/repo-releases/com/codahale/metrics/metrics-parent/3.0.0/metrics-parent-3.0.0.pom    Downloading: http://repo1.maven.org/maven2/com/codahale/metrics/metrics-parent/3.0.0/metrics-parent-3.0.0.pom    Downloaded: http://repo1.maven.org/maven2/com/codahale/metrics/metrics-parent/3.0.0/metrics-parent-3.0.0.pom (10 KB at 4.8 KB/sec)    Downloading: http://repo.akka.io/releases/com/codahale/metrics/metrics-jvm/3.0.0/metrics-jvm-3.0.0.pom    Downloading: http://scala-tools.org/repo-releases/com/codahale/metrics/metrics-jvm/3.0.0/metrics-jvm-3.0.0.pom    Downloading: http://repo1.maven.org/maven2/com/codahale/metrics/metrics-jvm/3.0.0/metrics-jvm-3.0.0.pom    Downloaded: http://repo1.maven.org/maven2/com/codahale/metrics/metrics-jvm/3.0.0/metrics-jvm-3.0.0.pom (965 B at 1.8 KB/sec)    Downloading: http://repo.akka.io/releases/com/codahale/metrics/metrics-json/3.0.0/metrics-json-3.0.0.pom    Downloading: http://scala-tools.org/repo-releases/com/codahale/metrics/metrics-json/3.0.0/metrics-json-3.0.0.pom    Downloading: http://repo1.maven.org/maven2/com/codahale/metrics/metrics-json/3.0.0/metrics-json-3.0.0.pom    Downloaded: http://repo1.maven.org/maven2/com/codahale/metrics/metrics-json/3.0.0/metrics-json-3.0.0.pom (2 KB at 2.6 KB/sec)    Downloading: http://repo.akka.io/releases/com/fasterxml/jackson/core/jackson-databind/2.2.2/jackson-databind-2.2.2.pom    Downloading: http://scala-tools.org/repo-releases/com/fasterxml/jackson/core/jackson-databind/2.2.2/jackson-databind-2.2.2.pom    Downloading: http://repo1.maven.org/maven2/com/fasterxml/jackson/core/jackson-databind/2.2.2/jackson-databind-2.2.2.pom    Downloaded: http://repo1.maven.org/maven2/com/fasterxml/jackson/core/jackson-databind/2.2.2/jackson-databind-2.2.2.pom (6 KB at 10.0 KB/sec)    Downloading: http://repo.akka.io/releases/com/fasterxml/jackson/core/jackson-annotations/2.2.2/jackson-annotations-2.2.2.pom    Downloading: http://scala-tools.org/repo-releases/com/fasterxml/jackson/core/jackson-annotations/2.2.2/jackson-annotations-2.2.2.pom    Downloading: http://repo1.maven.org/maven2/com/fasterxml/jackson/core/jackson-annotations/2.2.2/jackson-annotations-2.2.2.pom    Downloaded: http://repo1.maven.org/maven2/com/fasterxml/jackson/core/jackson-annotations/2.2.2/jackson-annotations-2.2.2.pom (2 KB at 2.4 KB/sec)    Downloading: http://repo.akka.io/releases/com/fasterxml/jackson/core/jackson-core/2.2.2/jackson-core-2.2.2.pom    Downloading: http://scala-tools.org/repo-releases/com/fasterxml/jackson/core/jackson-core/2.2.2/jackson-core-2.2.2.pom    Downloading: http://repo1.maven.org/maven2/com/fasterxml/jackson/core/jackson-core/2.2.2/jackson-core-2.2.2.pom    Downloaded: http://repo1.maven.org/maven2/com/fasterxml/jackson/core/jackson-core/2.2.2/jackson-core-2.2.2.pom (6 KB at 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[INFO] skip non existing resourceDirectory D:\all\idea\cloud-scale-bwamem-0.2.1\src\main\resources    [INFO]     [INFO] --- maven-scala-plugin:2.15.2:compile (default) @ cloud-scale-bwamem ---    [INFO] Checking for multiple versions of scala    [WARNING]  Expected all dependencies to require Scala version: 2.10.4    [WARNING]  cs.ucla.edu:cloud-scale-bwamem:0.2.0 requires scala version: 2.10.4    [WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:0.99.2 requires scala version: 2.10.4    [WARNING]  org.bdgenomics.adam:adam-core:0.14.0 requires scala version: 2.10.3    [WARNING] Multiple versions of scala libraries detected!    [INFO] includes = [**/*.scala,**/*.java,]    [INFO] excludes = []    [INFO] D:\all\idea\cloud-scale-bwamem-0.2.1\src\main\java:-1: info: compiling    [INFO] D:\all\idea\cloud-scale-bwamem-0.2.1\src\main\scala:-1: info: compiling    [INFO] Compiling 77 source files to D:\all\idea\cloud-scale-bwamem-0.2.1\target\classes at 1464961627035    [WARNING] warning: there were 22 deprecation warning(s); re-run with -deprecation for details    [WARNING] warning: there were 1 feature warning(s); re-run with -feature for details    [WARNING] two warnings found    [INFO] prepare-compile in 0 s    [INFO] compile in 88 s    [INFO]     [INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ cloud-scale-bwamem ---    [INFO] Changes detected - recompiling the module!    [WARNING] File encoding has not been set, using platform encoding UTF-8, i.e. build is platform dependent!    [INFO] Compiling 8 source files to D:\all\idea\cloud-scale-bwamem-0.2.1\target\classes    [INFO]     [INFO] --- maven-scala-plugin:2.15.2:compile (compile) @ cloud-scale-bwamem ---    [INFO] Checking for multiple versions of scala    [WARNING]  Expected all dependencies to require Scala version: 2.10.4    [WARNING]  cs.ucla.edu:cloud-scale-bwamem:0.2.0 requires scala version: 2.10.4    [WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:0.99.2 requires scala version: 2.10.4    [WARNING]  org.bdgenomics.adam:adam-core:0.14.0 requires scala version: 2.10.3    [WARNING] Multiple versions of scala libraries detected!    [INFO] includes = [**/*.scala,**/*.java,]    [INFO] excludes = []    [INFO] Nothing to compile - all classes are up to date    [INFO] ------------------------------------------------------------------------    [INFO] BUILD SUCCESS    [INFO] ------------------------------------------------------------------------    [INFO] Total time: 4:36.543s    [INFO] Finished at: Fri Jun 03 21:48:51 CST 2016    [INFO] Final Memory: 34M/380M    [INFO] ------------------------------------------------------------------------    Process finished with exit code 0

参考

【1】https://github.com/xubo245/AdamLearning【2】https://github.com/bigdatagenomics/adam/ 【3】https://github.com/xubo245/SparkLearning【4】http://spark.apache.org

研究成果：

【1】 [BIBM] Bo Xu, Changlong Li, Hang Zhuang, Jiali Wang, Qingfeng Wang, Chao Wang, and Xuehai Zhou, "Distributed Gene Clinical Decision Support System Based on Cloud Computing", in IEEE International Conference on Bioinformatics and Biomedicine. (BIBM 2017, CCF B)【2】 [IEEE CLOUD] Bo Xu, Changlong Li, Hang Zhuang, Jiali Wang, Qingfeng Wang, Xuehai Zhou. Efficient Distributed Smith-Waterman Algorithm Based on Apache Spark (CLOUD 2017, CCF-C).【3】 [CCGrid] Bo Xu, Changlong Li, Hang Zhuang, Jiali Wang, Qingfeng Wang, Jinhong Zhou, Xuehai Zhou. DSA: Scalable Distributed Sequence Alignment System Using SIMD Instructions. (CCGrid 2017, CCF-C).【4】more: https://github.com/xubo245/Publications

Help

If you have any questions or suggestions, please write it in the issue of this project or send an e-mail to me: [e-mail]: xu601450868QQ: 601450868