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  • UCSC AXTCHAIN installation error

    I am trying to install axtchain on my computer through the UCSC genome brower and I have MYSQL installed but I keep getting a error involving MYSQL library.

    Here is what I have done.


    ##edited .bashrc to include

    MACHTYPE=x86_64
    export MACHTYPE

    export MYSQLINC="/usr/local/mysql/include"
    export MYSQLLIBS="/usr/local/mysql/lib -mysqlclient -pthread "

    I got these directories using the command:

    mysql_config --libs
    will display the appropriate libraries to link with
    for your system configuration. And:
    mysql_config --include
    will display the appropriate MYSQLINC directory.


    MY GOAL was to install the hg folder and then the mousestuff folder so i can get axtchain

    I was able to get part of it set up but then ran into the following error.

    Last login: Mon Sep 23 10:57:18 on ttys000
    155-99-166-194:~ rebeccabruders$ cd /Users/rebeccabruders/scripts/kent
    155-99-166-194:kent rebeccabruders$ cd src
    155-99-166-194:src rebeccabruders$ cd hg
    155-99-166-194:hg rebeccabruders$ make
    cd lib && make
    make[1]: `../../lib/x86_64/jkhgap.a' is up to date.
    cd cartReset && echo cartReset && make
    cartReset
    gcc cartReset.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -pthread -L/lib -lssl -lcrypto -lpng -lm -L/usr/local/mysql/lib -mysqlclient -pthread -lstdc++ -lrt
    ld: library not found for -lrt
    collect2: ld returned 1 exit status
    make[1]: *** [compile] Error 1
    make: *** [cartReset.bins] Error 2
    155-99-166-194:hg rebeccabruders$


    I dont get where the -LRT is coming from since it isnt in my directory. Any help would be much appreciated.

  • #2
    Your system appears to be missing "real time extensions" library (librt). You should be able to locate and install that library.

    Comment


    • #3
      Real Time extension Library

      From what I can see this RT library is not available for Mac OS systems....

      Comment


      • #4
        You can download pre-compiled binaries (which includes axtchain) for Mac (kent utilities) here: http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/

        Comment


        • #5
          How do I unpack the files

          Im sorry this may be a stupid question but once I download the pre compiled binaries how do I run them. I tried many different things running them in my command line

          I tried just running the file

          155-99-216-224:~ rebeccabruders$ /Users/rebeccabruders/Downloads/axtChain
          -bash: /Users/rebeccabruders/Downloads/axtChain: Permission denied

          I tried using sudo and entered my password

          155-99-216-224:hg rebeccabruders$ sudo /Users/rebeccabruders/Downloads/axtChain sudo: /Users/rebeccabruders/Downloads/axtChain: command not found


          I tried adding make
          155-99-216-224:hg rebeccabruders$ sudo make /Users/rebeccabruders/Downloads/axtChain
          make: Nothing to be done for `/Users/rebeccabruders/Downloads/axtChain'.

          I tried to just type axtChain
          155-99-216-224:~ rebeccabruders$ axtChain
          -bash: axtChain: command not found

          Comment


          • #6
            You need to add "execute" permissions to the downloaded compiled files before they can be run. Do the following in a terminal:

            Code:
            $ cd /to_directory_where_the_downloaded_files_are_located
            $ chmod u+x * (if you only downloaded axtchain then chmod u+x axtchain)

            If you are trying to do this from a "regular" account you may need to use "sudo" before the chmod command.

            While running the program you can either use (./axtchain ,if you are in the directory where the program is located) or provide the full directory path to "axtchain" program ($/full_path_to/axtchain)
            Last edited by GenoMax; 09-24-2013, 07:53 AM.

            Comment


            • #7
              Thank you! I think I got it running!

              Comment

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