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  • BlatSrc 35 installing issue

    Im trying to install Blat on my ubuntu12.04 64bit following this steps:

    1. Download the BLAT source files at http://users.soe.ucsc.edu/~kent/src/ (look for the blatSrc* zip file with the most recent date)

    2. Unzip the archive to create a 'blatSrc' directory

    3. Remove the "-Werror" compiler flag to treat warnings as errors
    To do this, edit the newly extracted blatSrc/inc/common.mk file and remove all occurences of string "-Werror" (thus allowing to get past warnings as errors)
    Alternative [TO BE TESTED]:
    edit the blatSrc/inc/common.mk file and change only line 17 from

    HG_WARN_ERR = -DJK_WARN -Wall -Werror
    to
    HG_WARN_ERR = -DJK_WARN -Wall

    4. Check the value of the environment variable 'MACHTYPE' (which depends on machine architecture) by typing in a terminal:
    echo $MACHTYPE
    It's usually something like 'i386', 'i686' or 'x86_64'.
    If default $MACHTYPE is a long name with dashes (e.g. 'i486-pc-linux-gnu') it must be set to its correct "short" value. To find out this just type the command 'uname -m' and then:

    [Option 1, temporary change] [TO BE TESTED]
    Type the following commands:
    MACHTYPE=i686 (or the correct MACHTYPE)
    export MACHTYPE

    [Option 2, permanent change]
    Append the following two lines to the '~/.bashrc' file:
    MACHTYPE=i686 (or the correct MACHTYPE)
    export MACHTYPE

    5. Make the directory ~/bin/$MACHTYPE (which is where the non-web executables will go) by typing:
    mkdir ~/bin/$MACHTYPE

    6. Go to the blatSrc/lib directory. If it doesn't already exist, make also here a $MACHINE directory:
    mkdir $MACHTYPE

    7. At the blatSrc directory type 'make'.


    But once I start the make command and after the compiling process start the result I ger is :

    /usr/bin/ld: cannot open output file /root/bin/x86_64/blat: No such file or directory
    collect2: ld returned 1 exit status
    make[1]: *** [blat] Error 1
    make[1]: Leaving directory `/home/mohamed/Downloads/blatSrc/blat'
    make: *** [all] Error 2

    While the directory is already exist inside /root/bin/ by using the command:

    mkdir ~/bin/$MACHTYPE

    Which will not work this way but I have to acces the root folder after that the bin folder then creat the directory otherwise if I just eenter the command (mkdir ~/bin/$MACHTYPE) the result will be

    mkdir: cannot create directory `/root/bin/x86_64': No such file or directory

    How to solve it.

    Thank you in advance

  • #2
    Why are you root ?

    You should install userland apps as a normal user.


    Originally posted by Life_Dogma View Post
    Im trying to install Blat on my ubuntu12.04 64bit following this steps:

    1. Download the BLAT source files at http://users.soe.ucsc.edu/~kent/src/ (look for the blatSrc* zip file with the most recent date)

    2. Unzip the archive to create a 'blatSrc' directory

    3. Remove the "-Werror" compiler flag to treat warnings as errors
    To do this, edit the newly extracted blatSrc/inc/common.mk file and remove all occurences of string "-Werror" (thus allowing to get past warnings as errors)
    Alternative [TO BE TESTED]:
    edit the blatSrc/inc/common.mk file and change only line 17 from

    HG_WARN_ERR = -DJK_WARN -Wall -Werror
    to
    HG_WARN_ERR = -DJK_WARN -Wall

    4. Check the value of the environment variable 'MACHTYPE' (which depends on machine architecture) by typing in a terminal:
    echo $MACHTYPE
    It's usually something like 'i386', 'i686' or 'x86_64'.
    If default $MACHTYPE is a long name with dashes (e.g. 'i486-pc-linux-gnu') it must be set to its correct "short" value. To find out this just type the command 'uname -m' and then:

    [Option 1, temporary change] [TO BE TESTED]
    Type the following commands:
    MACHTYPE=i686 (or the correct MACHTYPE)
    export MACHTYPE

    [Option 2, permanent change]
    Append the following two lines to the '~/.bashrc' file:
    MACHTYPE=i686 (or the correct MACHTYPE)
    export MACHTYPE

    5. Make the directory ~/bin/$MACHTYPE (which is where the non-web executables will go) by typing:
    mkdir ~/bin/$MACHTYPE

    6. Go to the blatSrc/lib directory. If it doesn't already exist, make also here a $MACHINE directory:
    mkdir $MACHTYPE

    7. At the blatSrc directory type 'make'.


    But once I start the make command and after the compiling process start the result I ger is :

    /usr/bin/ld: cannot open output file /root/bin/x86_64/blat: No such file or directory
    collect2: ld returned 1 exit status
    make[1]: *** [blat] Error 1
    make[1]: Leaving directory `/home/mohamed/Downloads/blatSrc/blat'
    make: *** [all] Error 2

    While the directory is already exist inside /root/bin/ by using the command:

    mkdir ~/bin/$MACHTYPE

    Which will not work this way but I have to acces the root folder after that the bin folder then creat the directory otherwise if I just eenter the command (mkdir ~/bin/$MACHTYPE) the result will be

    mkdir: cannot create directory `/root/bin/x86_64': No such file or directory

    How to solve it.

    Thank you in advance

    Comment


    • #3
      Look at these environmental variables :

      These are what I use when I set up my environment for playing with UCSC/kent code ...
      I run it from /app1/dnload/newersrc/ directory. I run with as a dot command so it's set in the current shell (you can write your own script and just cut'n'paste the script text to the command line(s) to get the same effect as a "dot" command). These are bash specific:


      export USER=gbrowser-test2
      export HOME=/app1/dnload/newersrc/
      export PATH=$PATH:/app1/dnload/newersrc/bin/x86_64
      export MACHTYPE=x86_64


      Looks like you need to set HOME to some place you can write to.
      It's using some default HOME which you (since you are a mere user and not the mighty root) can not write to.
      Last edited by Richard Finney; 08-16-2012, 03:04 PM.

      Comment


      • #4
        Dear Friends,
        I was installing BLAT in a linux MINT 13 system with MACHTYPE i686-linux-gnu and followed the instruction provided by SEB567 here in this forum. In this process i received the following error and not found any further remedy.
        OBTAINED ERROR MESSAGE:
        /usr/bin/ld.bfd.real: cannot open output file /home/acb07/bin/i686/blat: No such file or directory
        collect2: ld returned 1 exit status
        make[1]: *** [blat] Error 1
        make[1]: Leaving directory `/home/acb07/Desktop/blatSrc/blat'
        make: *** [all] Error 2


        Looking forward for your suggestions to overcome these errors and towards a successful installation.

        Comment


        • #5
          Originally posted by anithsreenidhi View Post
          Dear Friends,
          I was installing BLAT in a linux MINT 13 system with MACHTYPE i686-linux-gnu and followed the instruction provided by SEB567 here in this forum. In this process i received the following error and not found any further remedy.
          OBTAINED ERROR MESSAGE:
          /usr/bin/ld.bfd.real: cannot open output file /home/acb07/bin/i686/blat: No such file or directory
          collect2: ld returned 1 exit status
          make[1]: *** [blat] Error 1
          make[1]: Leaving directory `/home/acb07/Desktop/blatSrc/blat'
          make: *** [all] Error 2


          Looking forward for your suggestions to overcome these errors and towards a successful installation.
          The linker is unable to write the resulting file in /home/acb07/bin/i686/blat.

          The most likely explanation is that /home/acb07/bin/i686/ does not
          exist.

          Can you throw this command before:

          mkdir -p ~/bin/i686

          Then, repeat what you have done.

          Comment


          • #6
            Dear seb567,

            Thank you for your valuable comments and suggestion on my previous post. I was trying to install BLAT both as root and current user (i.e. acb07). I followed your instructions and the following error has come up while installing.

            ar: could not create temporary file whilst writing archive: No more archived files
            make[1]: *** [/jkweb.a] Error 1
            make[1]: Leaving directory `/home/acb07/Desktop/blatSrc/lib'
            make: *** [all] Error 2


            I could able to create the directory /home/acb07/bin/i686/blat. And was trying to execute the command 'make' in my current directory "acb07@acb07-G31M-ES2L ~/Desktop/blatSrc $". I also, edited the permissions to the both the directories that were created.

            Hoping a suggestion to overcome the errors.
            Last edited by anithsreenidhi; 11-16-2012, 10:54 PM. Reason: Highliging

            Comment

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