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Fusioninspector singularity container not working #594

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rannick opened this issue Dec 20, 2024 · 1 comment
Open

Fusioninspector singularity container not working #594

rannick opened this issue Dec 20, 2024 · 1 comment
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@rannick
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rannick commented Dec 20, 2024

Description of the bug

Install separately from star-fusion

Command used and terminal output

Relevant files

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@rannick rannick added the bug Something isn't working label Dec 20, 2024
@rannick rannick self-assigned this Dec 20, 2024
@atrigila
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it does not work for docker either:

  ERROR ~ Error executing process > 'FUSIONINSPECTOR (test)'
  
  Caused by:
    Process `FUSIONINSPECTOR (test)` terminated with an error exit status (127)
  
  
  Command executed:
  
    FusionInspector \
        --fusions fusion_targets.A.txt \
        --genome_lib ctat_genome_lib_build_dir \
        --left_fq rnaseq_1.fastq.gz --right_fq rnaseq_2.fastq.gz \
        --CPU 4 \
        -O . \
        --out_prefix test \
        --vis --STAR_xtra_params "--limitSjdbInsertNsj 1000000" --annotate --examine_coding_effect
    
    cat <<-END_VERSIONS > versions.yml
    "FUSIONINSPECTOR":
        STAR-Fusion: $(STAR-Fusion --version 2>&1 | grep -i 'version' | sed 's/STAR-Fusion version: //')
    END_VERSIONS
  
  Command exit status:
    127
  
  Command output:
    (empty)
  
  Command error:
    .command.sh: line 9: FusionInspector: command not found

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