Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

                              Latest Articles

                              Collapse

                              • seqadmin
                                Recent Advances in Sequencing Analysis Tools
                                by seqadmin


                                The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
                                05-06-2024, 07:48 AM
                              • seqadmin
                                Essential Discoveries and Tools in Epitranscriptomics
                                by seqadmin




                                The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
                                04-22-2024, 07:01 AM

                              ad_right_rmr

                              Collapse

                              News

                              Collapse

                              Topics Statistics Last Post
                              Started by seqadmin, 05-14-2024, 07:03 AM
                              0 responses
                              19 views
                              0 likes
                              Last Post seqadmin  
                              Started by seqadmin, 05-10-2024, 06:35 AM
                              0 responses
                              44 views
                              0 likes
                              Last Post seqadmin  
                              Started by seqadmin, 05-09-2024, 02:46 PM
                              0 responses
                              54 views
                              0 likes
                              Last Post seqadmin  
                              Started by seqadmin, 05-07-2024, 06:57 AM
                              0 responses
                              42 views
                              0 likes
                              Last Post seqadmin  
                              Working...
                              X