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  • can't make bedtools

    Hello all,
    I'm new and have no clue what I'm doing. I apologize for basic questions. Please be kind. I've installed Bedtools and am trying to use the "make" command but I get the error below:

    Building BEDTools:
    =========================================================
    DETECTED_VERSION = v2.20.1
    CURRENT_VERSION = v2.20.1
    * Creating BamTools API
    - Building in src/utils/bedFile
    make[1]: *** No rule to make target 'bedFile.h', needed by '../../../obj//bedFile.o'. Stop.
    Makefile:130: recipe for target 'src/utils/bedFile' failed
    make: *** [src/utils/bedFile] Error 2





    I'm certain I'm doing something stupid and I'd appreciate you guys pointing it out.

    Cheers.

  • #2
    Did you download the code from https://github.com/arq5x/bedtools2/releases and then are trying to use "make" to compile it? Make is not for installing the software. What OS are you using?

    Comment


    • #3
      Thank you for your reply, GenoMax.

      I downloaded using the instructions on the bedtools website:

      $ curl http://bedtools.googlecode.com/files/BEDTools.<version>.tar.gz > BEDTools.tar.gz
      $ tar -zxvf BEDTools.tar.gz
      $ cd BEDTools-<version>
      $ make

      I am using cygwin on windows 8 (which I hate but it's what I have).

      Comment


      • #4
        Did you install a compiler when you installed Cygwin (gcc, g++)?

        Comment


        • #5
          I did, following these instructions:

          Comment


          • #6
            Can you try to re-download the source tar file and try make again? I am wondering if source file was corrupted. Did you get any errors when you did tar -xvcf command?

            Comment


            • #7
              Hey Clueless_in_ct

              You can make life a lot easier on yourself by installing virtualbox, and throwing in an install of ubuntu or bio linux (has a lot of software already installed) . Or dual boot works too.

              Comment

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