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adam-submit fails with no Spark installation #857

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laserson opened this issue Oct 8, 2015 · 3 comments
Closed

adam-submit fails with no Spark installation #857

laserson opened this issue Oct 8, 2015 · 3 comments

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@laserson
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laserson commented Oct 8, 2015

If I don't set SPARK_HOME and I don't have spark-submit on my PATH, then adam-submit errors out early:

$ bin/adam-submit 
Using ADAM_MAIN=org.bdgenomics.adam.cli.ADAMMain

I believe it's because the subshell call to which spark-submit returns an error code and adam-submit calls set -e.
@laserson
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laserson commented Oct 8, 2015

cc @heuermh

@heuermh
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heuermh commented Oct 8, 2015

I thought you were the bash expert? ;)
I can confirm this happens on HEAD.

@heuermh
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heuermh commented Oct 8, 2015

After further investigation it doesn't appear to be caused by anything I added recently. Commenting out set -e does the trick, what is that for?

laserson added a commit to laserson/adam that referenced this issue Oct 8, 2015
@laserson
[ADAM-857] Corrected handling of env vars in bin scripts
5c275c6 
Because of `set -e`, the `which spark-submit` subshell command was causing the script to exit early.

Fixes bigdatagenomics#857.
@laserson laserson mentioned this issue Oct 8, 2015
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@heuermh @laserson