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adam-shell prints command trace to stdout #1154

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heuermh opened this Issue Sep 8, 2016 · 1 comment

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heuermh commented Sep 8, 2016

$ ./bin/adam-shell 
+++ dirname ./bin/adam-shell
++ cd ./bin/..
++ pwd
+ SCRIPT_DIR=/Users/xxx/working/adam
+ [[ -z '' ]]
+ [[ -n '' ]]
+ ADAM_CLI_JAR=
+ '[' -d /Users/xxx/working/adam/repo ']'
+ ASSEMBLY_DIR=/Users/xxx/working/adam/adam-assembly/target
++ ls -1 /Users/xxx/working/adam/adam-assembly/target
++ grep '^adam_[0-9A-Za-z\.-]*\.jar$'
++ grep -v javadoc
++ wc -l
+ num_jars='       1'
+ '[' '       1' -eq 0 ']'
++ ls -1 /Users/xxx/working/adam/adam-assembly/target
++ grep '^adam_[0-9A-Za-z\.-]*\.jar$'
++ grep -v javadoc
+ ASSEMBLY_JARS=adam_2.10-0.19.1-SNAPSHOT.jar
+ '[' '       1' -gt 1 ']'
+ ADAM_CLI_JAR=/Users/xxx/working/adam/adam-assembly/target/adam_2.10-0.19.1-SNAPSHOT.jar
+ '[' -z '' ']'
++ which spark-shell
+ SPARK_SHELL=/usr/local/bin/spark-shell
+ '[' -z /usr/local/bin/spark-shell ']'
+ echo 'Using SPARK_SHELL=/usr/local/bin/spark-shell'
Using SPARK_SHELL=/usr/local/bin/spark-shell
+ /usr/local/bin/spark-shell --conf spark.serializer=org.apache.spark.serializer.KryoSerializer --conf spark.kryo.registrator=org.bdgenomics.adam.serialization.ADAMKryoRegistrator --jars /Users/xxx/working/adam/adam-assembly/target/adam_2.10-0.19.1-SNAPSHOT.jar
...

set -x was added in a55d2cb for debugging I would assume, should this be removed or perhaps changed to set -e?

@heuermh heuermh modified the milestone: 0.20.0 Sep 8, 2016

fnothaft added a commit to fnothaft/adam that referenced this issue Sep 8, 2016

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fnothaft Sep 8, 2016

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D'oh! That's my bad.

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fnothaft commented Sep 8, 2016

D'oh! That's my bad.

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