基因数据处理99之SparkBWA修改下载文件

由于每次make都需要下载spark包,180M,所以在Make中将其注释掉了。

然后运行make:

hadoop@Mcnode1:~/xubo/tools/SparkBWA$ make
if [ ! -d "build" ]; then mkdir build; fi
gcc -c -g -Wall -Wno-unused-function -O2 -fPIC -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -I/usr/lib/jvm/jdk1.7.0/include -I/usr/lib/jvm/jdk1.7.0/include/linux ./src/bwa_jni.c -o build/bwa_jni.o -lrt  
./src/bwa_jni.c: In function ‘Java_BwaJni_bwa_1jni’:
./src/bwa_jni.c:55:21: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default]
          argvTmp[i] = (*env)->GetStringUTFChars(env, string, 0);
                     ^
make -C ./bwa/bwa-0.7.12
make[1]: Entering directory `/home/hadoop/xubo/tools/SparkBWA/bwa/bwa-0.7.12'
make[1]: Nothing to be done for `all'.
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 ..
updating: QSufSort.o (deflated 66%)
updating: bamlite.o (deflated 67%)
updating: bntseq.o (deflated 70%)
updating: bwa.o (deflated 70%)
updating: bwa_jni.o (deflated 70%)
updating: bwamem.o (deflated 70%)
updating: bwamem_extra.o (deflated 75%)
updating: bwamem_pair.o (deflated 65%)
updating: bwape.o (deflated 69%)
updating: bwase.o (deflated 68%)
updating: bwaseqio.o (deflated 67%)
updating: bwashm.o (deflated 70%)
updating: bwt.o (deflated 66%)
updating: bwt_gen.o (deflated 68%)
updating: bwt_lite.o (deflated 64%)
updating: bwtaln.o (deflated 71%)
updating: bwtgap.o (deflated 70%)
updating: bwtindex.o (deflated 71%)
updating: bwtsw2_aux.o (deflated 68%)
updating: bwtsw2_chain.o (deflated 64%)
updating: bwtsw2_core.o (deflated 70%)
updating: bwtsw2_main.o (deflated 72%)
updating: bwtsw2_pair.o (deflated 64%)
updating: fastmap.o (deflated 72%)
updating: is.o (deflated 65%)
updating: kopen.o (deflated 69%)
updating: kstring.o (deflated 65%)
updating: ksw.o (deflated 71%)
updating: kthread.o (deflated 65%)
updating: libbwa.so (deflated 64%)
updating: main.o (deflated 78%)
updating: malloc_wrap.o (deflated 70%)
updating: maxk.o (deflated 66%)
updating: pemerge.o (deflated 69%)
updating: utils.o (deflated 69%)
updating: Bwa.class (deflated 56%)
updating: BwaInterpreter$BigFastq2RDDDouble.class (deflated 52%)
updating: BwaInterpreter$BigFastq2RDDPartitionsDouble.class (deflated 50%)
updating: BwaInterpreter.class (deflated 54%)
updating: BwaJni.class (deflated 32%)
updating: BwaOptions.class (deflated 54%)
updating: BwaRDD$BwaAlignment.class (deflated 49%)
updating: BwaRDD.class (deflated 48%)
updating: BwaSeq.class (deflated 24%)
updating: FastqInputFormat.class (deflated 56%)
updating: FastqInputFormatDouble.class (deflated 56%)
updating: FastqRecordReader.class (deflated 50%)
updating: FastqRecordReaderDouble.class (deflated 50%)
updating: SparkBWA.class (deflated 23%)
updating: SparkBWA.jar (deflated 6%)
updating: paired.sh (deflated 56%)
updating: pairedGRCH38L1.sh (deflated 58%)
#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 ..
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 = /home/hadoop/cloud/hadoop-2.6.0/

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
【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
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