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  • Compiling cufflinks 0.9.x

    Hi,

    Where do I get bamlib? The http://randspringer.de/bam does not work.

    I am trying to compile new cufflinks and tophat and got the folloing message:

    ./configure
    ...
    checking for bamlib... configure: error: We could not detect the bam libraries (version or higher). If you have a staged bam library (still not installed) please specify $BAM_ROOT in your environment and do not give a PATH to --with-bam option. If you are sure you have bam installed, then check your version number looking in <bam/version.hpp>. See http://randspringer.de/bam for more documentation.

    Thanks in advance.

  • #2
    This is a problem with TopHat 1.1.0 as well which I have been trying to compile on a Solaris machine all morning. I thought for a moment it might have been BamTools (a C++ API for BAM files) but the version I found does not appear to have the appropriate headers. Has to be something else.

    Hopefully Cole will be able to provide an answer.

    Comment


    • #3
      That error message is incorrect and misleading - my apologies. I'll update the build scripts to make it right. In the meantime, I suggest you take a look at the "Getting started" page:

      http://cufflinks.cbcb.umd.edu/tutorial.html

      Which describes how to install the BAM libraries such that you build can Cufflinks.
      Last edited by Cole Trapnell; 10-04-2010, 08:12 AM.

      Comment


      • #4
        Thanks. I should have realized it would be simple.

        Comment


        • #5
          hey cole;

          I am still getting the error
          checking for bamlib... configure: error: We could not detect the bam libraries (version or higher). If you have a staged bam library (still not installed) please specify $BAM_ROOT in your environment and do not give a PATH to --with-bam option. If you are sure you have bam installed, then check your version number looking in <bam/version.hpp>. See http://randspringer.de/bam for more documentation.

          installing TOPHAT. I have SAMTOOLS installed, but in my home/bin as I do not have permission to install apps on the machine. I looked at the configure and it appears to be a problem with idenfying the version number. I tried using the with-bam option and setting BAM_ROOT to no avail. Help would be really appreciated.

          Previous versions of tophat were no problem.

          Cheers
          Dennis

          Comment


          • #6
            Actually, the answer is the same for Tophat as for Cufflinks;

            In my case, I just changed the instructions to use /home/user/bin/samtools

            Download the SAM tools
            Unpack the SAM tools tarball and cd to the SAM tools source directory.
            Build the SAM tools by typing make at the command line.
            Choose a directory into which you wish to copy the SAM tools binary, the included library libbam.a, and the library headers. A common choice is /usr/local/. (I used /home/user/bin/samtools)
            Copy libbam.a to the lib/ directory in the folder you've chosen above (e.g. /usr/local/lib/) - /home/user/bin/samtools/lib
            Create a directory called "bam" in the include/ directory (e.g. /usr/local/include/bam) /home/user/bin/samtools/include/bam
            Copy the headers (files ending in .h) to the include/bam directory you've created above (e.g. /usr/local/include/bam)
            Copy the samtools binary to some directory in your PATH.

            Comment


            • #7
              this is still not working for me, trying to install tophat 1.1.0
              I copied the samtools binary into $BASE/bin, which is in my PATH
              then I created $BASE/bin/lib
              and copied libbam.a into this folder
              then I created $BASE/bin/include/bam
              and copied all headers (*.h) into that folder.

              I still get


              checking for bamlib... configure: error: We could not detect the bam libraries (version or higher). If you have a staged bam library (still not installed) please specify $BAM_ROOT in your environment and do not give a PATH to --with-bam option. If you are sure you have bam installed, then check your version number looking in <bam/version.hpp>. See http://randspringer.de/bam for more documentation.

              when I configure tophat.

              I tried to set BAM_ROOT to any of the above folders but that didn't make a difference either. http://randspringer.de/bam doesn't exist.

              Comment


              • #8
                Diffculty in installing topHat/Cufflinks

                Cufflinks and topHat are wonderful softwares, I can't wait to use them on my RNA-seq analysis.
                I tried to install topHat from source code.
                I followed your instructions, and also install samtools again.
                It seems to me that libbam.a never created in my samtools directory, so I cannot add it to the topHat/cufflinks path.

                Comment


                • #9
                  it's working for me now. Turns out that I had to use the --with-bam option and I was confused by the error message which said not to use this option.
                  Anyway, here is what I did (basically the same as posted above):

                  I'm installing in $HOME/software
                  the executable will go in $HOME/software/bin

                  Code:
                  mkdir $HOME/software/bin/lib
                  
                  mkdir -p $HOME/software/bin/include/bam
                  Copy files from the samtools source into those new directories. I had downloaded and untar'ed samtools in $HOME/downloads:
                  Code:
                  cp $HOME/downloads/samtools-0.1.8/libbam.a $HOME/software/bin/lib
                  cp $HOME/downloads/samtools-0.1.8/*.h $HOME/software/bin/include/bam
                  
                  wget [url]http://tophat.cbcb.umd.edu/downloads/tophat-1.1.0.tar.gz[/url]
                  tar -xzvf tophat-1.1.0.tar.gz
                  cd tophat-1.1.0
                  ./configure --prefix=$HOME/software --with-bam=$HOME/software/bin
                  make
                  make install
                  now it's working fine.

                  Comment


                  • #10
                    I eventually downloaded samtools 1.0.7a and followed your instructions, then I downloaded binary of tophat.
                    It work (as it seems from running the test_data) .
                    thank you very much

                    Comment

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