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  • BEDtools v2.14.3 installation issue for OSX Lion? : bamToBed

    I have successfully installed and used BEDtools v2 several times on OSX 10.6 machines. However, I'm on a new machine running OSX 10.7.2 and keep getting the following errors in the "make all" building process :

    --------------------------------------

    - Building in src/bamToBed
    * compiling bamToBed.cpp
    * linking bamToBed
    ld: in ../utils//BamTools/lib//libbamtools.a, archive has no table of contents for architecture x86_64
    collect2: ld returned 1 exit status
    make[1]: *** [bamToBed] Error 1

    - Building in src/bedToBam
    * compiling bedToBam.cpp
    * linking bedToBam
    ld: in ../utils//BamTools/lib//libbamtools.a, archive has no table of contents for architecture x86_64
    collect2: ld returned 1 exit status
    make[1]: *** [bedToBam] Error 1

    .
    .
    .

    - Building in src/tagBam
    * compiling tagBamMain.cpp
    * compiling tagBam.cpp
    * linking tagBam
    ld: in ../utils//BamTools/lib//libbamtools.a, archive has no table of contents for architecture x86_64
    collect2: ld returned 1 exit status
    make[1]: *** [tagBam] Error 1

    .
    .
    .

    - Building in src/windowBed
    * compiling windowMain.cpp
    * compiling windowBed.cpp
    * linking windowBed
    ld: in ../utils//BamTools/lib//libbamtools.a, archive has no table of contents for architecture x86_64
    collect2: ld returned 1 exit status
    make[1]: *** [windowBed] Error 1

    --------------------------------------

    Afterwards, neither of these tools are found in /bin, and (unsurprisingly) the commands aren't working. I have Googled to no avail. For what it's worth, another similar Lion error occurred here : http://www.mail-archive.com/ape-proj.../msg04086.html

    I was looking forward to an easy install after tons of trouble with Tophat, Bowtie, Galaxy, Cufflinks, and Homer, but it's not my day.

    The entire "make all" log is attached. Any advice/experience is appreciated. Thanks in advance.
    Attached Files

  • #2
    Hi,

    Can't tell what is going on here, but if it helps, I can tell you I have no problem compiling Bedtools 2.14.3 on Lion. I use Homebrew(http://mxcl.github.com/homebrew/). I personally submitted formulas for most of the tools you are mentioning, others were already there and I'm only helping keeping them updated.

    Even when I don't see how it would be any different using Homebrew in this case, I think it would be good to give it a try. Is only:
    brew install bedtools tophat cufflinks bowtie

    Homer and Galaxy aren't in Homebrew. I hope Galaxy goes one day the route of 'pip install galaxy'. For Homer it should be easy to add a formula.

    Comment


    • #3
      Magic (so far)

      Thanks so much, Carlos. That tool is amazing. Facepalm to me for running across that days ago, but not reading enough into it to figure out your amazingly powerful command.

      It successfully installed everything, after a samtools linking step fix and canned brew doctor fixes for cufflinks. If these tools are now functional (minus databases, etc.), I am ecstatic.

      Now if only there was a homebrew for CentOS and our lab server...

      Comment

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