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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--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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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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--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/CHANGES.txt
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spark-1.6.1-bin-hadoop2.6/python/run-tests.py
spark-1.6.1-bin-hadoop2.6/python/test_support/
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spark-1.6.1-bin-hadoop2.6/examples/src/main/python/mllib/gaussian_mixture_model.py
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spark-1.6.1-bin-hadoop2.6/examples/src/main/python/mllib/binary_classification_metrics_example.py
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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
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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
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spark-1.6.1-bin-hadoop2.6/examples/src/main/scala/org/apache/spark/examples/mllib/TallSkinnySVD.scala
spark-1.6.1-bin-hadoop2.6/examples/src/main/scala/org/apache/spark/examples/mllib/DenseGaussianMixture.scala
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spark-1.6.1-bin-hadoop2.6/examples/src/main/scala/org/apache/spark/examples/mllib/RegressionMetricsExample.scala
spark-1.6.1-bin-hadoop2.6/examples/src/main/scala/org/apache/spark/examples/mllib/SampledRDDs.scala
spark-1.6.1-bin-hadoop2.6/examples/src/main/scala/org/apache/spark/examples/mllib/DecisionTreeClassificationExample.scala
spark-1.6.1-bin-hadoop2.6/examples/src/main/scala/org/apache/spark/examples/mllib/RandomRDDGeneration.scala
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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: [email protected]
Wechat: xu601450868
QQ: 601450868