DELETE FROM FAILURE_EVENT;
DELETE FROM RUNTIME_ATTRIBUTES;
DELETE FROM EXECUTION_INFO;
DELETE FROM SYMBOL;
DELETE FROM WORKFLOW_EXECUTION_AUX;
DELETE FROM EXECUTION_EVENT;
DELETE FROM EXECUTION;
scottfrazer
/ gist:2fc865fab8f200cf6bb9cf09eb0f1905
Created
April 13, 2016 16:17
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| . | |
| ├── htcondor | |
| │ ├── project | |
| │ └── src | |
| │ ├── main | |
| │ │ ├── java | |
| │ │ ├── resources | |
| │ │ ├── scala | |
| │ │ │ └── cromwell | |
| │ │ │ └── backend |
scottfrazer
/ gist:a0838aa2180e7972da84c4730975b9f5
Created
April 13, 2016 16:13
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| Apr 13 02:21:26 gce-cromwell-dev01 docker/cromwell-app[4123]: 2016-04-13 02:21:26,183 cromwell-system-akka.actor.default-dispatcher-47 INFO - WorkflowManagerActor submitWorkflow input id = None, effective id = 0790bc7e-bdc0-49f5-a255-54fe6caa9bbc | |
| Apr 13 02:21:26 gce-cromwell-dev01 docker/cromwell-app[4123]: 2016-04-13 02:21:26,185 cromwell-system-akka.actor.default-dispatcher-36 WARN - Unrecognized workflow option(s): account_name | |
| Apr 13 02:21:26 gce-cromwell-dev01 docker/cromwell-app[4123]: 2016-04-13 02:21:26,241 cromwell-system-akka.actor.default-dispatcher-36 INFO - WorkflowActor [UUID(0790bc7e)]: Start(Some(Actor[akka://cromwell-system/user/cromwell-service/Endpoint-endpointActorName7115701931068594/Endpoint-endpointActorName7115701931068594#-1335398672])) message received | |
| Apr 13 02:21:26 gce-cromwell-dev01 docker/cromwell-app[4123]: 2016-04-13 02:21:26,241 cromwell-system-akka.actor.default-dispatcher-47 INFO - JesBackend [UUID(0790bc7e)]: Creating authentication file for workflow 0790bc7e-bdc0-49f5 |
scottfrazer
/ example.wdl
Created
April 13, 2016 12:32
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| task wc { | |
| String str | |
| command { | |
| echo "${str}" | wc -c | |
| } | |
| output { | |
| Int count = read_int("stdout") - 1 | |
| } | |
| } |
scottfrazer
/ queries.md
Last active
April 1, 2016 18:07
scottfrazer
/ cleandb.sql
Last active
April 1, 2016 14:40
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| DELETE FROM failure_event; | |
| DELETE FROM runtime_attributes; | |
| DELETE FROM execution_info; | |
| DELETE FROM symbol; | |
| DELETE FROM workflow_execution_aux; | |
| DELETE FROM execution_event; | |
| DELETE FROM execution; | |
| DELETE FROM workflow_execution; | |
| ALTER TABLE failure_event AUTO_INCREMENT = 1; |
scottfrazer
/ cromtool.md
Created
March 22, 2016 20:15
Python command line utility for working with Cromwell in DSDE
scottfrazer
/ context_manager.py
Last active
March 22, 2016 14:14
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| class ExecutableTempFile: | |
| def __init__(self, someFile): | |
| self.theFile= someFile | |
| def __enter__(self): | |
| self.transLog= SecureLog( self.theFile ) | |
| return self.transLog | |
| def __exit__( self, type, value, tb ): | |
| if type is not None: | |
| pass # Exception occurred | |
| self.transLog.finalize() |
scottfrazer
/ gist:8ba52a13e48cbff8e370
Created
March 16, 2016 13:15
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| java.lang.ExceptionInInitializerError | |
| at cromwell.engine.workflow.WorkflowManagerActor.restartIncompleteWorkflows(WorkflowManagerActor.scala:397) | |
| at cromwell.engine.workflow.WorkflowManagerActor.preStart(WorkflowManagerActor.scala:97) | |
| at akka.actor.Actor$class.aroundPreStart(Actor.scala:472) | |
| at cromwell.engine.workflow.WorkflowManagerActor.aroundPreStart(WorkflowManagerActor.scala:85) | |
| at akka.actor.ActorCell.create(ActorCell.scala:580) | |
| at akka.actor.ActorCell.invokeAll$1_aroundBody2(ActorCell.scala:456) | |
| at akka.actor.ActorCell$AjcClosure3.run(ActorCell.scala:1) | |
| at org.aspectj.runtime.reflect.JoinPointImpl.proceed(JoinPointImpl.java:149) | |
| at akka.kamon.instrumentation.ActorSystemMessageInstrumentation$$anonfun$aroundSystemMessageInvoke$1.apply(ActorSystemMessageInstrumentation.scala:34) |
scottfrazer
/ .bashrc
Created
March 3, 2016 13:02
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| #!/usr/bin/bash -l | |
| function parse_hostname { | |
| echo $(uname -n | cut -f1 -d'.') | |
| } | |
| function parse_git_branch { | |
| if git update-index -q --refresh 2>/dev/null; git diff-index --quiet --cached HEAD --ignore-submodules -- 2>/dev/null && git diff-files --quiet --ignore-submodules 2>/dev/null | |
| then dirty="" | |
| else |
scottfrazer
/ gist:7ae8c3bca3bc45e429cf
Created
February 22, 2016 17:07
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| 16-02-19 22:52:31,493 cromwell-system-akka.actor.default-dispatcher-7 INFO - WorkflowActor [UUID(60d1afe2)]: ExecutionStoreCreated(Start(Some(Actor[akka://cromwell-system/user/cromwell-service/Endpoint-endpointActorName2416685706549335/Endpoint-endpointActorName2416685706549335#-1982900038]))) message received | |
| 16-02-19 22:55:38,085 cromwell-system-akka.actor.default-dispatcher-5 INFO - JES Run [UUID(60d1afe2):StripUnmappedBamSuffix:2]: Status change from Initializing to Running | |
| 16-02-19 22:56:02,356 cromwell-system-akka.actor.default-dispatcher-26 INFO - JES Run [UUID(60d1afe2):StripUnmappedBamSuffix:4]: Status change from Initializing to Running | |
| 16-02-19 23:02:41,207 cromwell-system-akka.actor.default-dispatcher-7 INFO - JES Run [UUID(60d1afe2):StripUnmappedBamSuffix:3]: Status change from Initializing to Running | |
| 16-02-19 23:03:53,065 cromwell-system-akka.actor.default-dispatcher-7 INFO - JES Run [UUID(60d1afe2):StripUnmappedBamSuffix:2]: Status change from Running to Success | |
| 16-02-19 23:03:53,778 cromw |