Bug report - GATK 3.1-1 is a tar bomb

Bug report: I just tried to install version 3.1-1 and all files extracted into the current directory.

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  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi there, I just tested the download and it's fine (no tar bomb). Can you tell me how you extracted the files? Was it via command line?

  • $ tar -jxvf ../GenomeAnalysisTK-3.1-1.tar.bz2 
    GenomeAnalysisTK.jar
    resources/CountReads.java
    resources/CountLoci.java
    resources/CheckPileup.java
    resources/Pileup.java
    resources/PrintReads.java
    resources/exampleFASTA.dict
    resources/exampleFASTA.fasta
    resources/exampleBAM.bam
    resources/exampleBAM.bam.bai
    resources/exampleFASTA.fasta.fai
    
  • dsenalikdsenalik Member
    edited March 2014
    $ tar -jxvf /programinstallers/GenomeAnalysisTK-2.5-2.tar.bz2
    GenomeAnalysisTK-2.5-2-gf57256b/
    GenomeAnalysisTK-2.5-2-gf57256b/resources/
    GenomeAnalysisTK-2.5-2-gf57256b/GenomeAnalysisTK.jar
    GenomeAnalysisTK-2.5-2-gf57256b/resources/CheckPileup.java
    GenomeAnalysisTK-2.5-2-gf57256b/resources/CountLoci.java
    GenomeAnalysisTK-2.5-2-gf57256b/resources/CountReads.java
    GenomeAnalysisTK-2.5-2-gf57256b/resources/Pileup.java
    GenomeAnalysisTK-2.5-2-gf57256b/resources/PrintReads.java
    GenomeAnalysisTK-2.5-2-gf57256b/resources/exampleBAM.bam
    GenomeAnalysisTK-2.5-2-gf57256b/resources/exampleBAM.bam.bai
    GenomeAnalysisTK-2.5-2-gf57256b/resources/exampleFASTA.dict
    GenomeAnalysisTK-2.5-2-gf57256b/resources/exampleFASTA.fasta
    GenomeAnalysisTK-2.5-2-gf57256b/resources/exampleFASTA.fasta.fai
    
  • Perhaps tar bomb was harsh. Still, more than one file in the current directory, and behavior is different than previously.

  • Perhaps the distribution could consist of just a (versioned) jar file, with a separate download of a resources tarball? I definitely agree with the sentiment that expanding a tar shouldn't endanger my existing files, and it seems like the resources are only likely to be used (once) by brand new users. Without the resources, there's only one file to distribute, which means no surprises when it's used. And since jars are (usually) compressed, there's no need to manipulate the file at all for download.

    I may be an edge case, but I must have at least a dozen copies of that resources dir in my various GenomeAnalysisTK-x.y-z directories.

    As an aside - the search bar at the top of the page might have sensitivity issues. I searched for the very memorable and likely unique phrase "tar bomb", and got no results. I ended up having to scroll down the list manually to find this thread

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    You know, I kind of hate that resources directory myself. The contents are of extremely limited utility (and in some cases, misleading). If this is a common sentiment, I'm more than happy to lobby for getting rid of it altogether.

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