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  • TopHat installation

    I was trying to install TopHat on my Mac Osx machine. The configuration results from ./configure for TopHat are:

    -- tophat 1.3.3 Configuration Results --
    C compiler: gcc -Wall -Wno-strict-aliasing -arch x86_64 -O3 -DNDEBUG
    C++ compiler: g++ -Wall -Wno-strict-aliasing -arch x86_64 -O3 -DNDEBUG -I/Users/vmittal3/usr/local/include
    GCC version: gcc (GCC) 4.6.0
    Host System type: i686-apple-darwin10.6.0
    Install prefix: /Users/vmittal3/usr/local
    Install eprefix: ${prefix}

    See config.h for further configuration information.
    Email <[email protected]> with questions and bug reports.


    It works fine till this point but once I do "make", it terminates with the following errors:

    make all-recursive
    Making all in src
    if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/local/include -Wall -Wno-strict-aliasing -arch x86_64 -O3 -DNDEBUG -I/Users/me_user/usr/local/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -arch x86_64 -O3 -DNDEBUG -I/Users/me_user/usr/local/include -MT reads.o -MD -MP -MF ".deps/reads.Tpo" -c -o reads.o reads.cpp; \
    then mv -f ".deps/reads.Tpo" ".deps/reads.Po"; else rm -f ".deps/reads.Tpo"; exit 1; fi
    g++: error: x86_64: No such file or directory
    g++: error: x86_64: No such file or directory
    g++: error: unrecognized option '-arch'
    g++: error: unrecognized option '-arch'
    make[2]: *** [reads.o] Error 1
    make[1]: *** [all-recursive] Error 1
    make: *** [all] Error 2


    Any suggestions? Thanks.

  • #2
    Watch the -arch format, there use to be a typo in the manual not sure if it got fixed. These instruction have worked in the past (http://seqanswers.com/forums/showthr...?t=4589&page=3)

    Comment


    • #3
      Hi John,
      Thanks for the reply. Where is the typo.. could you please elaborate? Also, I couldn't find TopHat installation help on the link you provided.

      Comment


      • #4
        The tophat install instructions are on the #42 reply, second one. The typo in the old manual regarded the install of boost and how to note the x86_64 environment. Can't remember the exact specifics but it took me a while to figure out why it was not working.

        Regarding your problem
        1) Do you have Xcode install or are you using a different compiler?
        2) What machine are you using (looks like a Mac, if so as long as it has intel processors not old power PC the instructions on the thread have worked

        looks at the difference in config results

        Code:
         C compiler:          gcc -Wall -arch x86_64 -O3  -DNDEBUG
          C++ compiler:        g++ -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/jkeats/local/include
          GCC version:         i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5664)
          Host System type:    i386-apple-darwin10.8.0
          Install prefix:      /Users/jkeats/local
          Install eprefix:     ${prefix}

        Comment


        • #5
          I have being promoting Homebrew(http://mxcl.github.com/homebrew/) as an easy way to install tools on Mac OS X, I personally took into getting several formulas for the most common used tools approved. I test them in 'Snow Leopard' and 'Lion' and I try to keep them updated. If you decide to go this route, after install Homebrew, you could do something like:
          Code:
          brew install tophat
          There are a few other tools there already, among them:
          cufflinks
          bowtie
          samtools (which will get automatically installed as a dependency for tophat or cufflinks)
          tabix
          bwa
          plink
          velvet
          bedtools

          I would love to see this list to grow.

          Hope it helps,
          Carlos
          Last edited by Carlos Borroto; 11-21-2011, 09:46 AM.

          Comment


          • #6
            Hi John and Carlos,
            Thanks a lot for your help. Actually you are true John, there is an error in the Boost installation command on the TopHat manual page: "address_model" should be "address-model".
            For the mac installation, I figured that TopHat wasn't installing properly because of the mismatched system variables and their expected values between the TopHat config file and system variables (I am using Mac OSx 10.6).
            Configure file expects "-arch x86_64" while my system had actually "-march=x86-64". I replaced it in the TopHat config file and then the compilation was successful.

            Comment

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