基因数据处理93之sparkBWA安装和使用

1.安装

git clone https://github.com/citiususc/SparkBWA.git
cd SparkBWA
make

2.使用:
报错:没有成功

hadoop@Master:~/xubo/project/alignment/sparkBWA$ ./run.sh 
Error: Must specify a primary resource (JAR or Python or R file)
Run with --help for usage help or --verbose for debug output
./run.sh: line 5: --executor-memory: command not found
./run.sh: line 11: -index: command not found
hadoop@Master:~/xubo/project/alignment/sparkBWA$ vi run.sh 
hadoop@Master:~/xubo/project/alignment/sparkBWA$ ./run.sh 
Error: Must specify a primary resource (JAR or Python or R file)
Run with --help for usage help or --verbose for debug output
./run.sh: line 5: --executor-memory: command not found
./run.sh: line 13: -index: command not found
hadoop@Master:~/xubo/project/alignment/sparkBWA$ vi run.sh 
hadoop@Master:~/xubo/project/alignment/sparkBWA$ ls
run.sh  SparkBWA.jar
hadoop@Master:~/xubo/project/alignment/sparkBWA$ ./run.sh 
Error: Must specify a primary resource (JAR or Python or R file)
Run with --help for usage help or --verbose for debug output
./run.sh: line 5: --executor-memory: command not found
./run.sh: line 13: -index: command not found
hadoop@Master:~/xubo/project/alignment/sparkBWA$ vi run.sh 
hadoop@Master:~/xubo/project/alignment/sparkBWA$ ./run.sh 
Error: Must specify a primary resource (JAR or Python or R file)
Run with --help for usage help or --verbose for debug output
./run.sh: line 5: --executor-memory: command not found
./run.sh: line 14: /home/hadoop/xubo/data/alignment/bwa/datatest.fa: Permission denied
hadoop@Master:~/xubo/project/alignment/sparkBWA$ vi run.sh 
hadoop@Master:~/xubo/project/alignment/sparkBWA$ ./run.sh 
Error: Must specify a primary resource (JAR or Python or R file)
Run with --help for usage help or --verbose for debug output
./run.sh: line 7: --archives: command not found
./run.sh: line 14: /home/hadoop/xubo/data/alignment/bwa/datatest.fa: Permission denied
hadoop@Master:~/xubo/project/alignment/sparkBWA$ ll
total 36
drwxrwxr-x 2 hadoop hadoop  4096  6月 12 18:56 ./
drwxrwxr-x 4 hadoop hadoop  4096  6月 12 18:28 ../
-rwxr-xr-x 1 hadoop hadoop   453  6月 12 18:56 run.sh*
-rw-rw-r-- 1 hadoop hadoop 22906  6月 12 18:29 SparkBWA.jar
hadoop@Master:~/xubo/project/alignment/sparkBWA$ vi run.sh 
hadoop@Master:~/xubo/project/alignment/sparkBWA$ ./run.sh 
Error: Must specify a primary resource (JAR or Python or R file)
Run with --help for usage help or --verbose for debug output
./run.sh: line 9: --verbose: command not found
./run.sh: line 14: /home/hadoop/xubo/data/alignment/bwa/datatest.fa: Permission denied
hadoop@Master:~/xubo/project/alignment/sparkBWA$ 

参考:
【1】 https://github.com/citiususc/SparkBWA

安装记录:

gcc -c -g -Wall -Wno-unused-function -O2 -fPIC -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtgap.c -o bwtgap.o
gcc -c -g -Wall -Wno-unused-function -O2 -fPIC -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtaln.c -o bwtaln.o
gcc -c -g -Wall -Wno-unused-function -O2 -fPIC -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bamlite.c -o bamlite.o
gcc -c -g -Wall -Wno-unused-function -O2 -fPIC -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  is.c -o is.o
gcc -c -g -Wall -Wno-unused-function -O2 -fPIC -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtindex.c -o bwtindex.o
gcc -c -g -Wall -Wno-unused-function -O2 -fPIC -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwape.c -o bwape.o
gcc -c -g -Wall -Wno-unused-function -O2 -fPIC -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  kopen.c -o kopen.o
gcc -c -g -Wall -Wno-unused-function -O2 -fPIC -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  pemerge.c -o pemerge.o
gcc -c -g -Wall -Wno-unused-function -O2 -fPIC -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  maxk.c -o maxk.o
gcc -c -g -Wall -Wno-unused-function -O2 -fPIC -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtsw2_core.c -o bwtsw2_core.o
gcc -c -g -Wall -Wno-unused-function -O2 -fPIC -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtsw2_main.c -o bwtsw2_main.o
gcc -c -g -Wall -Wno-unused-function -O2 -fPIC -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtsw2_aux.c -o bwtsw2_aux.o
gcc -c -g -Wall -Wno-unused-function -O2 -fPIC -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwt_lite.c -o bwt_lite.o
gcc -c -g -Wall -Wno-unused-function -O2 -fPIC -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtsw2_chain.c -o bwtsw2_chain.o
gcc -c -g -Wall -Wno-unused-function -O2 -fPIC -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  fastmap.c -o fastmap.o
gcc -c -g -Wall -Wno-unused-function -O2 -fPIC -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtsw2_pair.c -o bwtsw2_pair.o
gcc -c -g -Wall -Wno-unused-function -O2 -fPIC -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  main.c -o main.o
gcc -g -Wall -Wno-unused-function -O2 -fPIC -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o is.o bwtindex.o bwape.o kopen.o pemerge.o maxk.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread -lrt
make[1]: Leaving directory `/home/hadoop/xubo/tools/SparkBWA/bwa/bwa-0.7.12'
if [ ! -d "build" ]; then mkdir build; fi
cp ./bwa/bwa-0.7.12/*.o build
gcc -shared -o build/libbwa.so build/*.o -lrt 
cd build && zip -r bwa ./* && cd ..
  adding: QSufSort.o (deflated 66%)
  adding: bamlite.o (deflated 67%)
  adding: bntseq.o (deflated 70%)
  adding: bwa.o (deflated 70%)
  adding: bwa_jni.o (deflated 70%)
  adding: bwamem.o (deflated 70%)
  adding: bwamem_extra.o (deflated 75%)
  adding: bwamem_pair.o (deflated 65%)
  adding: bwape.o (deflated 69%)
  adding: bwase.o (deflated 68%)
  adding: bwaseqio.o (deflated 68%)
  adding: bwashm.o (deflated 70%)
  adding: bwt.o (deflated 67%)
  adding: bwt_gen.o (deflated 68%)
  adding: bwt_lite.o (deflated 65%)
  adding: bwtaln.o (deflated 71%)
  adding: bwtgap.o (deflated 70%)
  adding: bwtindex.o (deflated 71%)
  adding: bwtsw2_aux.o (deflated 68%)
  adding: bwtsw2_chain.o (deflated 64%)
  adding: bwtsw2_core.o (deflated 70%)
  adding: bwtsw2_main.o (deflated 72%)
  adding: bwtsw2_pair.o (deflated 64%)
  adding: fastmap.o (deflated 72%)
  adding: is.o (deflated 65%)
  adding: kopen.o (deflated 69%)
  adding: kstring.o (deflated 65%)
  adding: ksw.o (deflated 71%)
  adding: kthread.o (deflated 65%)
  adding: libbwa.so (deflated 64%)
  adding: main.o (deflated 78%)
  adding: malloc_wrap.o (deflated 70%)
  adding: maxk.o (deflated 66%)
  adding: pemerge.o (deflated 69%)
  adding: utils.o (deflated 69%)
cd ./libs && wget http://ftp.cixug.es/apache/spark/spark-1.6.1/spark-1.6.1-bin-hadoop2.6.tgz && tar xzvf spark-1.6.1-bin-hadoop2.6.tgz && cp spark-1.6.1-bin-hadoop2.6/lib/spark-assembly-1.6.1-hadoop2.6.0.jar ./ && rm -Rf spark-1.6.1-bin-hadoop2.6 && rm spark-1.6.1-bin-hadoop2.6.tgz && cd ..
--2016-06-12 16:46:09--  http://ftp.cixug.es/apache/spark/spark-1.6.1/spark-1.6.1-bin-hadoop2.6.tgz
Resolving ftp.cixug.es (ftp.cixug.es)... 193.144.61.75
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HTTP request sent, awaiting response... 200 OK
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Saving to: ‘spark-1.6.1-bin-hadoop2.6.tgz’

39% [==========================================================>                                                                                           ] 114,566,890 28.6KB/s   in 26m 13s

2016-06-12 17:12:29 (71.1 KB/s) - Connection closed at byte 114566890. Retrying.

--2016-06-12 17:12:30--  (try: 2)  http://ftp.cixug.es/apache/spark/spark-1.6.1/spark-1.6.1-bin-hadoop2.6.tgz
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41% [+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++==>                                                                                        ] 120,833,451 11.9KB/s   in 3m 47s 

2016-06-12 17:16:19 (26.9 KB/s) - Connection closed at byte 120833451. Retrying.

--2016-06-12 17:16:21--  (try: 3)  http://ftp.cixug.es/apache/spark/spark-1.6.1/spark-1.6.1-bin-hadoop2.6.tgz
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46% [++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++=======>                                                                                ] 135,476,692 8.89KB/s   in 7m 54s 

2016-06-12 17:24:16 (30.1 KB/s) - Connection closed at byte 135476692. Retrying.

--2016-06-12 17:24:19--  (try: 4)  http://ftp.cixug.es/apache/spark/spark-1.6.1/spark-1.6.1-bin-hadoop2.6.tgz
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58% [++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++================>                                                               ] 169,085,837 28.2KB/s   in 12m 46s

2016-06-12 17:37:06 (42.8 KB/s) - Connection closed at byte 169085837. Retrying.

--2016-06-12 17:37:10--  (try: 5)  http://ftp.cixug.es/apache/spark/spark-1.6.1/spark-1.6.1-bin-hadoop2.6.tgz
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2016-06-12 18:06:24 (67.0 KB/s) - ‘spark-1.6.1-bin-hadoop2.6.tgz’ saved [289405702/289405702]

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spark-1.6.1-bin-hadoop2.6/NOTICE
spark-1.6.1-bin-hadoop2.6/CHANGES.txt
spark-1.6.1-bin-hadoop2.6/python/
spark-1.6.1-bin-hadoop2.6/python/run-tests.py
spark-1.6.1-bin-hadoop2.6/python/test_support/
spark-1.6.1-bin-hadoop2.6/python/test_support/userlibrary.py
spark-1.6.1-bin-hadoop2.6/python/test_support/userlib-0.1.zip
spark-1.6.1-bin-hadoop2.6/python/test_support/sql/
spark-1.6.1-bin-hadoop2.6/python/test_support/sql/people.json
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spark-1.6.1-bin-hadoop2.6/python/test_support/sql/orc_partitioned/b=1/c=1/.part-r-00000-829af031-b970-49d6-ad39-30460a0be2c8.orc.crc
spark-1.6.1-bin-hadoop2.6/python/test_support/sql/orc_partitioned/_SUCCESS
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spark-1.6.1-bin-hadoop2.6/python/test_support/sql/orc_partitioned/b=0/c=0/.part-r-00000-829af031-b970-49d6-ad39-30460a0be2c8.orc.crc
spark-1.6.1-bin-hadoop2.6/python/test_support/sql/text-test.txt
spark-1.6.1-bin-hadoop2.6/python/test_support/sql/parquet_partitioned/
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spark-1.6.1-bin-hadoop2.6/python/test_support/sql/parquet_partitioned/_SUCCESS
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spark-1.6.1-bin-hadoop2.6/examples/src/main/python/ml/standard_scaler_example.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/ml/vector_assembler_example.py
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spark-1.6.1-bin-hadoop2.6/examples/src/main/python/ml/cross_validator.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/ml/simple_text_classification_pipeline.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/ml/dataframe_example.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/ml/decision_tree_regression_example.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/ml/linear_regression_with_elastic_net.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/ml/index_to_string_example.py
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spark-1.6.1-bin-hadoop2.6/examples/src/main/python/ml/multilayer_perceptron_classification.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/ml/gradient_boosted_tree_classifier_example.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/ml/kmeans_example.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/ml/pca_example.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/ml/polynomial_expansion_example.py
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spark-1.6.1-bin-hadoop2.6/examples/src/main/python/ml/aft_survival_regression.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/ml/rformula_example.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/ml/logistic_regression_with_elastic_net.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/ml/decision_tree_classification_example.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/ml/tokenizer_example.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/ml/random_forest_classifier_example.py
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spark-1.6.1-bin-hadoop2.6/examples/src/main/python/ml/vector_indexer_example.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/ml/normalizer_example.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/ml/bucketizer_example.py
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spark-1.6.1-bin-hadoop2.6/examples/src/main/python/ml/elementwise_product_example.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/ml/tf_idf_example.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/ml/word2vec_example.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/pagerank.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/wordcount.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/pi.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/hbase_inputformat.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/logistic_regression.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/cassandra_outputformat.py
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spark-1.6.1-bin-hadoop2.6/examples/src/main/python/streaming/network_wordcount.py
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spark-1.6.1-bin-hadoop2.6/examples/src/main/python/streaming/flume_wordcount.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/transitive_closure.py
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spark-1.6.1-bin-hadoop2.6/examples/src/main/python/avro_inputformat.py
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spark-1.6.1-bin-hadoop2.6/examples/src/main/python/mllib/sampled_rdds.py
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spark-1.6.1-bin-hadoop2.6/examples/src/main/python/mllib/multi_class_metrics_example.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/mllib/naive_bayes_example.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/mllib/decision_tree_regression_example.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/mllib/ranking_metrics_example.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/mllib/gaussian_mixture_model.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/mllib/gradient_boosting_regression_example.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/mllib/binary_classification_metrics_example.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/mllib/logistic_regression.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/mllib/isotonic_regression_example.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/mllib/word2vec.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/mllib/multi_label_metrics_example.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/mllib/kmeans.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/mllib/decision_tree_classification_example.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/mllib/random_rdd_generation.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/mllib/random_forest_classification_example.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/mllib/correlations.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/parquet_inputformat.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/hbase_outputformat.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/als.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/sql.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/sort.py
spark-1.6.1-bin-hadoop2.6/examples/src/main/python/cassandra_inputformat.py
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spark-1.6.1-bin-hadoop2.6/examples/src/main/java/org/apache/spark/examples/ml/JavaAFTSurvivalRegressionExample.java
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spark-1.6.1-bin-hadoop2.6/examples/src/main/java/org/apache/spark/examples/ml/JavaRandomForestRegressorExample.java
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spark-1.6.1-bin-hadoop2.6/examples/src/main/java/org/apache/spark/examples/ml/JavaCountVectorizerExample.java
spark-1.6.1-bin-hadoop2.6/examples/src/main/java/org/apache/spark/examples/ml/JavaRFormulaExample.java
spark-1.6.1-bin-hadoop2.6/examples/src/main/java/org/apache/spark/examples/ml/JavaOneHotEncoderExample.java
spark-1.6.1-bin-hadoop2.6/examples/src/main/java/org/apache/spark/examples/ml/JavaQuantileDiscretizerExample.java
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spark-1.6.1-bin-hadoop2.6/examples/src/main/java/org/apache/spark/examples/ml/JavaGradientBoostedTreeClassifierExample.java
spark-1.6.1-bin-hadoop2.6/examples/src/main/java/org/apache/spark/examples/ml/JavaMultilayerPerceptronClassifierExample.java
spark-1.6.1-bin-hadoop2.6/examples/src/main/java/org/apache/spark/examples/ml/JavaNGramExample.java
spark-1.6.1-bin-hadoop2.6/examples/src/main/java/org/apache/spark/examples/ml/JavaStandardScalerExample.java
spark-1.6.1-bin-hadoop2.6/examples/src/main/java/org/apache/spark/examples/ml/JavaDecisionTreeClassificationExample.java
spark-1.6.1-bin-hadoop2.6/examples/src/main/java/org/apache/spark/examples/ml/JavaNormalizerExample.java
spark-1.6.1-bin-hadoop2.6/examples/src/main/java/org/apache/spark/examples/ml/JavaPolynomialExpansionExample.java
spark-1.6.1-bin-hadoop2.6/examples/src/main/java/org/apache/spark/examples/ml/JavaBinarizerExample.java
spark-1.6.1-bin-hadoop2.6/examples/src/main/java/org/apache/spark/examples/ml/JavaGradientBoostedTreeRegressorExample.java
spark-1.6.1-bin-hadoop2.6/examples/src/main/java/org/apache/spark/examples/ml/JavaStringIndexerExample.java
spark-1.6.1-bin-hadoop2.6/examples/src/main/java/org/apache/spark/examples/ml/JavaWord2VecExample.java
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spark-1.6.1-bin-hadoop2.6/examples/src/main/java/org/apache/spark/examples/ml/JavaElementwiseProductExample.java
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spark-1.6.1-bin-hadoop2.6/examples/src/main/java/org/apache/spark/examples/streaming/JavaSqlNetworkWordCount.java
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spark-1.6.1-bin-hadoop2.6/examples/src/main/java/org/apache/spark/examples/JavaHdfsLR.java
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spark-1.6.1-bin-hadoop2.6/examples/src/main/java/org/apache/spark/examples/mllib/JavaPrefixSpanExample.java
spark-1.6.1-bin-hadoop2.6/examples/src/main/java/org/apache/spark/examples/mllib/JavaDecisionTreeRegressionExample.java
spark-1.6.1-bin-hadoop2.6/examples/src/main/java/org/apache/spark/examples/mllib/JavaAssociationRulesExample.java
spark-1.6.1-bin-hadoop2.6/examples/src/main/java/org/apache/spark/examples/mllib/JavaBinaryClassificationMetricsExample.java
spark-1.6.1-bin-hadoop2.6/examples/src/main/java/org/apache/spark/examples/mllib/JavaRandomForestClassificationExample.java
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spark-1.6.1-bin-hadoop2.6/examples/src/main/scala/org/apache/spark/examples/mllib/TallSkinnySVD.scala
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spark-1.6.1-bin-hadoop2.6/examples/src/main/scala/org/apache/spark/examples/mllib/RegressionMetricsExample.scala
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spark-1.6.1-bin-hadoop2.6/R/lib/SparkR/Meta/Rd.rds
spark-1.6.1-bin-hadoop2.6/R/lib/SparkR/profile/
spark-1.6.1-bin-hadoop2.6/R/lib/SparkR/profile/general.R
spark-1.6.1-bin-hadoop2.6/R/lib/SparkR/profile/shell.R
spark-1.6.1-bin-hadoop2.6/R/lib/SparkR/worker/
spark-1.6.1-bin-hadoop2.6/R/lib/SparkR/worker/daemon.R
spark-1.6.1-bin-hadoop2.6/R/lib/SparkR/worker/worker.R
spark-1.6.1-bin-hadoop2.6/R/lib/SparkR/NAMESPACE
spark-1.6.1-bin-hadoop2.6/R/lib/SparkR/tests/
spark-1.6.1-bin-hadoop2.6/R/lib/SparkR/tests/testthat/
spark-1.6.1-bin-hadoop2.6/R/lib/SparkR/tests/testthat/test_textFile.R
spark-1.6.1-bin-hadoop2.6/R/lib/SparkR/tests/testthat/jarTest.R
spark-1.6.1-bin-hadoop2.6/R/lib/SparkR/tests/testthat/test_client.R
spark-1.6.1-bin-hadoop2.6/R/lib/SparkR/tests/testthat/test_includeJAR.R
spark-1.6.1-bin-hadoop2.6/R/lib/SparkR/tests/testthat/test_broadcast.R
spark-1.6.1-bin-hadoop2.6/R/lib/SparkR/tests/testthat/test_binaryFile.R
spark-1.6.1-bin-hadoop2.6/R/lib/SparkR/tests/testthat/test_rdd.R
spark-1.6.1-bin-hadoop2.6/R/lib/SparkR/tests/testthat/packageInAJarTest.R
spark-1.6.1-bin-hadoop2.6/R/lib/SparkR/tests/testthat/test_sparkSQL.R
spark-1.6.1-bin-hadoop2.6/R/lib/SparkR/tests/testthat/test_parallelize_collect.R
spark-1.6.1-bin-hadoop2.6/R/lib/SparkR/tests/testthat/test_includePackage.R
spark-1.6.1-bin-hadoop2.6/R/lib/SparkR/tests/testthat/test_shuffle.R
spark-1.6.1-bin-hadoop2.6/R/lib/SparkR/tests/testthat/test_Serde.R
spark-1.6.1-bin-hadoop2.6/R/lib/SparkR/tests/testthat/test_mllib.R
spark-1.6.1-bin-hadoop2.6/R/lib/SparkR/tests/testthat/test_binary_function.R
spark-1.6.1-bin-hadoop2.6/R/lib/SparkR/tests/testthat/test_context.R
spark-1.6.1-bin-hadoop2.6/R/lib/SparkR/tests/testthat/test_take.R
spark-1.6.1-bin-hadoop2.6/R/lib/SparkR/tests/testthat/test_utils.R
spark-1.6.1-bin-hadoop2.6/licenses/
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-slf4j.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-scalacheck.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-py4j.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-paranamer.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-netlib.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-Mockito.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-minlog.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-graphlib-dot.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-d3.min.js.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-f2j.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-junit-interface.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-boto.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-spire.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-pyrolite.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-xmlenc.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-scala.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-SnapTree.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-AnchorJS.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-jline.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-jblas.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-heapq.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-cloudpickle.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-reflectasm.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-jpmml-model.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-javolution.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-jbcrypt.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-sbt-launch-lib.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-kryo.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-DPark.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-scopt.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-sorttable.js.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-dagre-d3.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-jquery.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-protobuf.txt
spark-1.6.1-bin-hadoop2.6/licenses/LICENSE-antlr.txt
spark-1.6.1-bin-hadoop2.6/ec2/
spark-1.6.1-bin-hadoop2.6/ec2/spark_ec2.py
spark-1.6.1-bin-hadoop2.6/ec2/README
spark-1.6.1-bin-hadoop2.6/ec2/spark-ec2
spark-1.6.1-bin-hadoop2.6/ec2/deploy.generic/
spark-1.6.1-bin-hadoop2.6/ec2/deploy.generic/root/
spark-1.6.1-bin-hadoop2.6/ec2/deploy.generic/root/spark-ec2/
spark-1.6.1-bin-hadoop2.6/ec2/deploy.generic/root/spark-ec2/ec2-variables.sh
spark-1.6.1-bin-hadoop2.6/conf/
spark-1.6.1-bin-hadoop2.6/conf/fairscheduler.xml.template
spark-1.6.1-bin-hadoop2.6/conf/metrics.properties.template
spark-1.6.1-bin-hadoop2.6/conf/spark-env.sh.template
spark-1.6.1-bin-hadoop2.6/conf/log4j.properties.template
spark-1.6.1-bin-hadoop2.6/conf/docker.properties.template
spark-1.6.1-bin-hadoop2.6/conf/slaves.template
spark-1.6.1-bin-hadoop2.6/conf/spark-defaults.conf.template
spark-1.6.1-bin-hadoop2.6/LICENSE
spark-1.6.1-bin-hadoop2.6/bin/
spark-1.6.1-bin-hadoop2.6/bin/spark-shell
spark-1.6.1-bin-hadoop2.6/bin/spark-submit.cmd
spark-1.6.1-bin-hadoop2.6/bin/spark-shell2.cmd
spark-1.6.1-bin-hadoop2.6/bin/pyspark
spark-1.6.1-bin-hadoop2.6/bin/sparkR.cmd
spark-1.6.1-bin-hadoop2.6/bin/spark-class2.cmd
spark-1.6.1-bin-hadoop2.6/bin/run-example.cmd
spark-1.6.1-bin-hadoop2.6/bin/spark-submit2.cmd
spark-1.6.1-bin-hadoop2.6/bin/spark-class
spark-1.6.1-bin-hadoop2.6/bin/spark-submit
spark-1.6.1-bin-hadoop2.6/bin/spark-sql
spark-1.6.1-bin-hadoop2.6/bin/run-example
spark-1.6.1-bin-hadoop2.6/bin/beeline
spark-1.6.1-bin-hadoop2.6/bin/pyspark2.cmd
spark-1.6.1-bin-hadoop2.6/bin/spark-shell.cmd
spark-1.6.1-bin-hadoop2.6/bin/spark-class.cmd
spark-1.6.1-bin-hadoop2.6/bin/pyspark.cmd
spark-1.6.1-bin-hadoop2.6/bin/sparkR
spark-1.6.1-bin-hadoop2.6/bin/beeline.cmd
spark-1.6.1-bin-hadoop2.6/bin/sparkR2.cmd
spark-1.6.1-bin-hadoop2.6/bin/run-example2.cmd
spark-1.6.1-bin-hadoop2.6/bin/load-spark-env.sh
spark-1.6.1-bin-hadoop2.6/bin/load-spark-env.cmd
spark-1.6.1-bin-hadoop2.6/lib/
spark-1.6.1-bin-hadoop2.6/lib/datanucleus-core-3.2.10.jar
spark-1.6.1-bin-hadoop2.6/lib/spark-assembly-1.6.1-hadoop2.6.0.jar
spark-1.6.1-bin-hadoop2.6/lib/datanucleus-api-jdo-3.2.6.jar
spark-1.6.1-bin-hadoop2.6/lib/datanucleus-rdbms-3.2.9.jar
spark-1.6.1-bin-hadoop2.6/lib/spark-1.6.1-yarn-shuffle.jar
spark-1.6.1-bin-hadoop2.6/lib/spark-examples-1.6.1-hadoop2.6.0.jar
spark-1.6.1-bin-hadoop2.6/README.md
javac -cp ./libs/commons-cli-1.2.jar:./libs/spark-assembly-1.6.1-hadoop2.6.0.jar -d build -Xlint:none ./src/*.java
cd build && jar cfe SparkBWA.jar SparkBWA ./*.class && cd ..
#cd build && jar cfe SparkBWASeq.jar BwaSeq ./*.class && cd ..
================================================================================
SparkBWA has been compiled.
Location    = /home/hadoop/xubo/tools/SparkBWA/build/
JAVA_HOME   = /usr/lib/jvm/jdk1.7.0
HADOOP_HOME = 
================================================================================
hadoop@Master:~/xubo/tools/SparkBWA$ 
hadoop@Master:~/xubo/tools/SparkBWA$ 

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
【5】http://stackoverflow.com/questions/28166667/how-to-pass-d-parameter-or-environment-variable-to-spark-job  
【6】http://stackoverflow.com/questions/28840438/how-to-override-sparks-log4j-properties-per-driver

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: xubo245@mail.ustc.edu.cn
Wechat: xu601450868
QQ: 601450868
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