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Oshlack / Slinker

Slinker offers a succinct and complementary method to visualise RNA-Seq data through superTranscripts.
MIT License
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Unable to run test data after install #2

Open prm123342 opened 2 years ago

prm123342 commented 2 years ago

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:

                      No such property: temp_source in stage make_dir

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

breons commented 2 years ago

Sorry about the delay on this!

The most recent commit resolves this issue. Let me know how you go.