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} missing at the end of cromwell.example.backends/SGE.conf #7007

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lindenb opened this issue Feb 8, 2023 · 0 comments · May be fixed by #7008
Open

} missing at the end of cromwell.example.backends/SGE.conf #7007

lindenb opened this issue Feb 8, 2023 · 0 comments · May be fixed by #7008

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@lindenb
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lindenb commented Feb 8, 2023

Hi , I'm new to cromwell/wdl. I tried to run a workflow using a SGE backend.

wget -O SGE.conf "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/cromwell.example.backends/SGE.conf"

$ java  -Dconfig.file=${PWD}/SGE.conf -jar  ${CROMWELL_JAR} run test.wdl --inputs input.json 
Exception in thread "main" java.lang.ExceptionInInitializerError
	at cromwell.CromwellApp$.runCromwell(CromwellApp.scala:14)
	at cromwell.CromwellApp$.delayedEndpoint$cromwell$CromwellApp$1(CromwellApp.scala:25)
	at cromwell.CromwellApp$delayedInit$body.apply(CromwellApp.scala:3)
	at scala.Function0.apply$mcV$sp(Function0.scala:39)
	at scala.Function0.apply$mcV$sp$(Function0.scala:39)
	at scala.runtime.AbstractFunction0.apply$mcV$sp(AbstractFunction0.scala:17)
	at scala.App.$anonfun$main$1(App.scala:76)
	at scala.App.$anonfun$main$1$adapted(App.scala:76)
	at scala.collection.IterableOnceOps.foreach(IterableOnce.scala:563)
	at scala.collection.IterableOnceOps.foreach$(IterableOnce.scala:561)
	at scala.collection.AbstractIterable.foreach(Iterable.scala:926)
	at scala.App.main(App.scala:76)
	at scala.App.main$(App.scala:74)
	at cromwell.CromwellApp$.main(CromwellApp.scala:3)
	at cromwell.CromwellApp.main(CromwellApp.scala)
Caused by: com.typesafe.config.ConfigException$Parse: /home/lindenbaum-p/notebook/2023/20230208.wdl/SGE.conf: 60: expecting a close parentheses ')' here, not: end of file
	at com.typesafe.config.impl.ConfigDocumentParser$ParseContext.parseError(ConfigDocumentParser.java:201)
	at com.typesafe.config.impl.ConfigDocumentParser$ParseContext.parseError(ConfigDocumentParser.java:197)
	at com.typesafe.config.impl.ConfigDocumentParser$ParseContext.parseKey(ConfigDocumentParser.java:279)

adding an extra } at the end of SGE.conf fixed the problem. I'll submit a PR if I'm not wrong.
lindenb added a commit to lindenb/cromwell that referenced this issue Feb 8, 2023
@lindenb
adding extra '}'
bf6b5e5 
If I'm not wrong this should fix broadinstitute#7007 .
@lindenb lindenb linked a pull request Feb 8, 2023 that will close this issue
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adding extra '}' in SGE.conf lindenb/cromwell
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