GCDSS: Distributed Gene Clinical Decision Support System Based on Cloud Computing
####1.1 Preparing: we should prepare before run GCDSS.
- Apache Spark : https://github.com/apache/spark
- Alluxio: http://www.alluxio.org/
- HDFS: https://github.com/apache/hadoop
##2.build mvn -DskipTests clean package ##3.run
spark-submit --class com.github.xubo245.gcdss.adam.postProcessing.ReadPostProcessing \
--master spark://MaspterIP:7077 \
--conf "spark.executor.extraJavaOptions=-Djava.library.path=/home/hadoop/disk2/xubo/lib/" \
--jars /home/hadoop/cloud/adam/lib/adam_2.10-0.23.0-SNAPSHOT.jar \
--executor-memory 20G \
GCDSS.jar \
$1 $2 $3 $4
Parameter:
$1: operate type, such as markDuplicate,sort,BQSR，realignIndel
$2: reads file location
$3: output path
For Example:
for num in 2000000 10000000 20000000
do
for i in {1..5}
do
fq='/xubo/project/alignment/CloudBWA/g38/time/cloudBWAnewg38L50c'$num'Nhs20Paired12time10num16k1.adam'
out='/xubo/project/alignment/CloudBWA/g38/time/cloudBWAnewg38L50c'$num'Nhs20Paired12time10num16k1.markDuplicateI'$i'.adam'
vcf='/xubo/callVariant/vcf/vcfSelectAddSequenceDictionaryWithChr.adam'
hadoop fs -rm -R -f $out
sh testReadPostProcessing.sh "markDuplicate" $fq $out $vcf
hadoop fs -rm -R -f $out
done
done
more shell example in sh file
CloudBWA is a distributed read mapping algorithms in GCDSS
The code of CloudBWA in another github project: CloudBWA
the Tutorial or docs is being written.
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]
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