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Oshlack / JAFFA

JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions
https://github.com/Oshlack/JAFFA/wiki
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Installation issues #85

Closed skudashev closed 2 years ago

skudashev commented 2 years ago

Hello Jaffa creators, thank you for such a cool tool. I am currently trying to install and run it on our cluster via the docker image: singularity pull docker://quay.io/biocontainers/jaffa:2.3--hdfd78af_0 However, when I try running it with singularity exec ~/jaffa_2.3--hdfd78af_0.sif bpipe run JAFFA-version-2.3/JAFFAL.groovy ~/fastqs/*fastq.gz I get this error: 

=========================================== Bpipe Error ============================================

An error occurred executing your pipeline:

- Error evaluating script '/ei/projects/8/8289c66d-2d56-4706-a307-5a9a3eb3747e/data/JAFFA-version-2.3/JAFFA_stages.groovy': A script, requested to be loaded from file '/ei/projects/8/8289c66d-2d56-4706-a307-5a9a3eb3747e/data/JAFFA-version-2.3/tools.groovy', could not be accessed.

Please see the details below for more information.

========================================== Error Details ===========================================

bpipe.PipelineError: Error evaluating script '/ei/projects/8/8289c66d-2d56-4706-a307-5a9a3eb3747e/data/JAFFA-version-2.3/JAFFA_stages.groovy': A script, requested to be loaded from file '/ei/projects/8/8289c66d-2d56-4706-a307-5a9a3eb3747e/data/JAFFA-version-2.3/tools.groovy', could not be accessed.
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    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 JAFFAL.groovy.run(JAFFAL.groovy:14)
    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)

Does this mean I need to try installing via the ./install_linux64.sh route?

Kind regards,

Sofia