20170203 Add two shell scripts"

example/config.txt

@@ -1,15 +1,15 @@
 # it is assumed that this file exists on HDFS already
 # File name must have a dot inside
-BAM_FILE: /bamfiles/child_hg19_SVs_v2_chr21.sort.bam
+BAM_FILE: /bamfiles/child_hg19_SVs_v2.sort.bam
 # this is the local path to the corresponding VCF. Change accordingly.
-VCF_FILE: VCF/cov20_loh.vcf
+VCF_FILE: VCF/cov40.vcf
 # following are the pipeline components that should be run.
-RUN_DEPTH_CALLER: false
+RUN_DEPTH_CALLER: true
 RUN_GLOBAL_SORT: false
-INIT_VCF_LOOKUP: false
-RUN_BINNER: false
-RUN_CNV_CALLER: false
-RUN_SR_PE_EXTRACTER: true
+INIT_VCF_LOOKUP: true
+RUN_BINNER: true
+RUN_CNV_CALLER: true
+RUN_SR_PE_EXTRACTER: false
 # We want the number of BAM file reducers to be approximately equal
 # to the number of mappers (which is a function of the BAM file size).
 # e.g. 800

example/run.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
 hdfs dfs -rm -r workdir
 hadoop jar ../target/penncnv-seq-0.1.jar edu.usc.PennCnvSeq -libjars $HADOOP_CLASSPATH config.txt
-#hadoop jar ../target/penncnv-seq-0.1.jar edu.usc.PennCnvSeq -libjars $HADOOP_BAM/target/hadoop-bam-7.0.1-SNAPSHOT-jar-with-dependencies.jar config.txt
+#hadoop jar ../target/penncnv-seq-0.1.jar edu.usc.PennCnvSeq -libjars $HADOOP_BAM/target/hadoop-bam-7.1.0-jar-with-dependencies.jar config.txt
 hdfs dfs -getmerge workdir/cnv/$BAM_FILENAME/* results.txt

pom.xml

@@ -16,10 +16,10 @@
     <name>cnv-caller</name>
     <description>A CNV caller based on sequence reads.</description>
     <properties>
-        <java.version>1.7.0_55</java.version>
+        <java.version>1.7.0_51</java.version>
         <htsjdk.version>1.118</htsjdk.version>
         <!-- CHANGE THIS FOR A DIFFERENT VERSION OF HADOOP -->
-        <hadoop.version>2.6.0</hadoop.version>
+        <hadoop.version>2.7.3</hadoop.version>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     </properties>
     <build>

resource/make_users.sh

@@ -1,8 +1,8 @@
 USERS=('huiyang' 'hadoop')
-hdfs dfs -mkdir /home
+hdfs dfs -mkdir /user
 for user in "${USERS[@]}"
 do
-    hdfs dfs -mkdir /home/$user
+    hdfs dfs -mkdir /user/$user
 done