When running the test data after installation I obtain this error (I have both manually set the environment paths and tried via updating the tools.groovy without any luck fixing this).
====================================== Stage make_dir (cases) ======================================
WARNING: An error occurred evaluating your pipeline stage: groovy.lang.MissingPropertyException: No such property: temp_source in stage make_dir. Please see Bpipe log file for full details.
groovy.lang.MissingPropertyException: No such property: temp_source in stage make_dir
at bpipe.PipelineDelegate.propertyMissing(PipelineDelegate.groovy:265)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at bpipe.PipelineDelegate.getProperty(PipelineDelegate.groovy)
at slinker$_run_closure2$_closure17.doCall(slinker.groovy:161)
at slinker$_run_closure2$_closure17.doCall(slinker.groovy)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at bpipe.PipelineContext.produceImpl(PipelineContext.groovy:1369)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at bpipe.PipelineContext.invokeMethod(PipelineContext.groovy)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at bpipe.PipelineDelegate.methodMissing(PipelineDelegate.groovy:155)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at bpipe.PipelineDelegate.invokeMethod(PipelineDelegate.groovy)
at slinker$_run_closure2.doCall(slinker.groovy:160)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at bpipe.PipelineStage.invokeMethod(PipelineStage.groovy)
at bpipe.PipelineStage$_runWrappedBody_closure5.doCall(PipelineStage.groovy:434)
at bpipe.PipelineStage$_runWrappedBody_closure5.doCall(PipelineStage.groovy)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at bpipe.PipelineStage.runWrappedBody(PipelineStage.groovy:433)
at bpipe.PipelineStage.runBody(PipelineStage.groovy:407)
at bpipe.PipelineStage.run(PipelineStage.groovy:243)
at bpipe.PipelineCategory$_plus_closure5.doCall(PipelineCategory.groovy:227)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at bpipe.PipelineStage.invokeMethod(PipelineStage.groovy)
at bpipe.PipelineStage$_runWrappedBody_closure5.doCall(PipelineStage.groovy:434)
at bpipe.PipelineStage$_runWrappedBody_closure5.doCall(PipelineStage.groovy)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at bpipe.PipelineStage.runWrappedBody(PipelineStage.groovy:433)
at bpipe.PipelineStage.runBody(PipelineStage.groovy:407)
at bpipe.PipelineStage.run(PipelineStage.groovy:243)
at bpipe.PipelineStage$run.call(Unknown Source)
at bpipe.Pipeline.runSegment(Pipeline.groovy:664)
at bpipe.BranchRunner.run(BranchRunner.groovy:69)
groovy.lang.MissingPropertyException: No such property: temp_source in stage make_dir
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at slinker.groovy$_run_closure2$_closure17.doCall(slinker.groovy:161)
at slinker.groovy$_run_closure2$_closure17.doCall(slinker.groovy)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at slinker.groovy$_run_closure2.doCall(slinker.groovy:160)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
When running the test data after installation I obtain this error (I have both manually set the environment paths and tried via updating the tools.groovy without any luck fixing this).
(slinker) qbi-paulm:Enviro uqpmars3$ bpipe -p case_sample=$SLINKERDIR/tests/unhealthy_Aligned.sortedByCoord.out.bam -p gene=ETV6 -p genome=19 -p a_mem=20000000000 -p g_mem=20000000000 -p results=$PWD -p threads=4 $SLINKERDIR/workflows/slinker.groovy $SLINKERDIR/tests/*.bam ╒══════════════════════════════════════════════════════════════════════════════════════════════════╕ | Starting Pipeline at 2022-01-18 15:03 | ╘══════════════════════════════════════════════════════════════════════════════════════════════════╛
====================================== Stage make_dir (cases) ====================================== WARNING: An error occurred evaluating your pipeline stage: groovy.lang.MissingPropertyException: No such property: temp_source in stage make_dir. Please see Bpipe log file for full details. groovy.lang.MissingPropertyException: No such property: temp_source in stage make_dir at bpipe.PipelineDelegate.propertyMissing(PipelineDelegate.groovy:265) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at bpipe.PipelineDelegate.getProperty(PipelineDelegate.groovy) at slinker$_run_closure2$_closure17.doCall(slinker.groovy:161) at slinker$_run_closure2$_closure17.doCall(slinker.groovy) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at bpipe.PipelineContext.produceImpl(PipelineContext.groovy:1369) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at bpipe.PipelineContext.invokeMethod(PipelineContext.groovy) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at bpipe.PipelineDelegate.methodMissing(PipelineDelegate.groovy:155) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at bpipe.PipelineDelegate.invokeMethod(PipelineDelegate.groovy) at slinker$_run_closure2.doCall(slinker.groovy:160) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at bpipe.PipelineStage.invokeMethod(PipelineStage.groovy) at bpipe.PipelineStage$_runWrappedBody_closure5.doCall(PipelineStage.groovy:434) at bpipe.PipelineStage$_runWrappedBody_closure5.doCall(PipelineStage.groovy) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at bpipe.PipelineStage.runWrappedBody(PipelineStage.groovy:433) at bpipe.PipelineStage.runBody(PipelineStage.groovy:407) at bpipe.PipelineStage.run(PipelineStage.groovy:243) at bpipe.PipelineCategory$_plus_closure5.doCall(PipelineCategory.groovy:227) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at bpipe.PipelineStage.invokeMethod(PipelineStage.groovy) at bpipe.PipelineStage$_runWrappedBody_closure5.doCall(PipelineStage.groovy:434) at bpipe.PipelineStage$_runWrappedBody_closure5.doCall(PipelineStage.groovy) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at bpipe.PipelineStage.runWrappedBody(PipelineStage.groovy:433) at bpipe.PipelineStage.runBody(PipelineStage.groovy:407) at bpipe.PipelineStage.run(PipelineStage.groovy:243) at bpipe.PipelineStage$run.call(Unknown Source) at bpipe.Pipeline.runSegment(Pipeline.groovy:664) at bpipe.BranchRunner.run(BranchRunner.groovy:69)
=========================================== Bpipe Error ============================================
An error occurred executing your pipeline:
Please see the details below for more information.
========================================== Error Details ===========================================
groovy.lang.MissingPropertyException: No such property: temp_source in stage make_dir at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at slinker.groovy$_run_closure2$_closure17.doCall(slinker.groovy:161) at slinker.groovy$_run_closure2$_closure17.doCall(slinker.groovy) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at slinker.groovy$_run_closure2.doCall(slinker.groovy:160) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
====================================================================================================
More details about why this error occurred may be available in the full log file .bpipe/bpipe.log