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  • Cufflink installation problem for Linux

    Hey Guys,
    I am trying to install "Cufflink" in Linux machine but it is throwing an error "Cannot execute.exe file" every time, I try to execute Cufflinks.exe or any other exe files.

    Please help me if anyone know how to handle this..

    Thank you.

  • #2
    I think .exe file is for windows, not Linux. I'm not a Linux guy and I'm not sure.

    Comment


    • #3
      Originally posted by DrD2009 View Post
      Hey Guys,
      I am trying to install "Cufflink" in Linux machine but it is throwing an error "Cannot execute.exe file" every time, I try to execute Cufflinks.exe or any other exe files.

      Please help me if anyone know how to handle this..

      Thank you.
      Make sure you get the Linux binary:

      -drd

      Comment


      • #4
        It's a Linux Binary but it is not working.

        Can someone please write step wise commands/procedure to make it work!!

        Thank you

        Comment


        • #5
          step wise

          Download cufflinks-0.8.1.Linux_x86_64.tar.gz
          Untar it: tar xvfz cufflinks-0.8.1.Linux_x86_64.tar.gz
          Move cufflinks and cuffcompare to your PATH.

          Comment


          • #6
            Originally posted by BioTalk View Post
            It's a Linux Binary but it is not working.

            Can someone please write step wise commands/procedure to make it work!!

            Thank you
            How do you know it's a Linux Binary? Where did you get it?
            Xi Wang

            Comment


            • #7
              Originally posted by Boel View Post
              Download cufflinks-0.8.1.Linux_x86_64.tar.gz
              Untar it: tar xvfz cufflinks-0.8.1.Linux_x86_64.tar.gz
              Move cufflinks and cuffcompare to your PATH.
              Here is the step wise method what I did :

              1. I downloaded Cufflinks-0.8.1.Linux_x86_64.tar.gz
              2. Untar Cufflinks-0.8.1.Linux_x86_64.tar.gz
              3. Moved cufflinks and cuffcompare to the path
              4. tried to execute Cufflinks and cuffcompare with ./cufflinks and ./cuffcompare respectively.
              5. Also I tried to give input of sam file with the command cuffliinks test_data.sam

              But it is throwing the error "Cannot execute binary file" every time I write any command. Please let me know if there are some other commands to work with it.

              Thank you

              Comment


              • #8
                Originally posted by BioTalk View Post
                Here is the step wise method what I did :

                1. I downloaded Cufflinks-0.8.1.Linux_x86_64.tar.gz
                2. Untar Cufflinks-0.8.1.Linux_x86_64.tar.gz
                3. Moved cufflinks and cuffcompare to the path
                4. tried to execute Cufflinks and cuffcompare with ./cufflinks and ./cuffcompare respectively.
                5. Also I tried to give input of sam file with the command cuffliinks test_data.sam

                But it is throwing the error "Cannot execute binary file" every time I write any command. Please let me know if there are some other commands to work with it.

                Thank you

                EDIT: you may use the 32-bit system. I just tried a 32 bit system, it threw this error.
                you should download the source code, and compile it yourself.
                Last edited by Xi Wang; 02-16-2010, 07:56 AM.
                Xi Wang

                Comment


                • #9
                  Originally posted by Xi Wang View Post
                  You need to change the files executable by the command chmod.
                  With the command Chmod I came to know that the file is executable, but I dont know the exact command, I should write to execute it.

                  Comment


                  • #10
                    32- Bit system..How can I try it?

                    Thank you

                    Comment


                    • #11
                      Originally posted by BioTalk View Post
                      32- Bit system..How can I try it?

                      Thank you
                      * Download this package:


                      * Untar the package
                      * cd the dir cufflinks-0.8.1
                      * type ./configure
                      * type make
                      * type make install

                      If no error, it is installed successfully.
                      Xi Wang

                      Comment


                      • #12
                        Originally posted by Xi Wang View Post
                        * Download this package:


                        * Untar the package
                        * cd the dir cufflinks-0.8.1
                        * type ./configure
                        * type make
                        * type make install

                        If no error, it is installed successfully.
                        Thanks Xi Wang. Looks like it is working but I got an error in the middle of installation that "We could not detect the boost lib with version 1.38 or higher."

                        So I tried to find Boost library for Linux, but it looks like there isn't any or probably any spececific out of the list.


                        Thank you.

                        Comment


                        • #13
                          For boost, download this file


                          And follow the instruction in the dir after untar the package.
                          Xi Wang

                          Comment


                          • #14
                            Hey Guys,

                            I am still not able to configure cufflinks. It is constantly throwing me an error eventhough I downloaded and latest version of boost and tryed to add it to its path:

                            The error is: "We could not detect the boost library(version1.38 or higher). If you have a stages boost library(still not installed) please specify $boost_root in your envireonment and do not give a PATH to --with-bost option. IF you are sure you have boost installed, then check 7youe version number looking in<boost/version.hpp>"

                            I think I am doing some silly mistake but don't know what? PLease write stepwise command so that my cufflinks starts working...!!

                            Comment


                            • #15
                              Originally posted by BioTalk View Post
                              Hey Guys,

                              I am still not able to configure cufflinks. It is constantly throwing me an error eventhough I downloaded and latest version of boost and tryed to add it to its path:

                              The error is: "We could not detect the boost library(version1.38 or higher). If you have a stages boost library(still not installed) please specify $boost_root in your envireonment and do not give a PATH to --with-bost option. IF you are sure you have boost installed, then check 7youe version number looking in<boost/version.hpp>"

                              I think I am doing some silly mistake but don't know what? PLease write stepwise command so that my cufflinks starts working...!!
                              The software requires the Boost library (C++). Did you download the library prior to try to configure the software?
                              -drd

                              Comment

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