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  • Rabia Faizan
    replied
    urgent

    need help in Glimmer installation please its urgent

      Leave a comment:

    • Rabia Faizan
      replied
      i need help

        Leave a comment:

      • GenoMax
        replied
        Originally posted by Bioinform View Post
        HI,

        I am having a problem with glimmer3.

        -bash: ./g3-from-scratch.csh: Permission denied

        Help would be appreciated

        Thanks
        You probably do not have execute permissions on that script. Do the following
        Code:
        $ chmod u+x ./g3-from-scratch.csh

          Leave a comment:

        • Bioinform
          replied
          -bash: ./g3-from-scratch.csh: Permission denied

          Originally posted by Votinhkiem90 View Post
          Yes, I know, but I don't know how to compile it.
          However, all tool in the /glimmer3.02/bin still normally running? when I want to run g3-from,... in Scipts express this error.
          hmm
          HI,

          I am having a problem with glimmer3.

          -bash: ./g3-from-scratch.csh: Permission denied

          Help would be appreciated

          Thanks

            Leave a comment:

          • Votinhkiem90
            replied
            Originally posted by GenoMax View Post
            I just realized that you compiled the software in a new location. So the directory you would want to check would be
            Yes, I know, but I don't know how to compile it.
            However, all tool in the /glimmer3.02/bin still normally running? when I want to run g3-from,... in Scipts express this error.
            hmm

              Leave a comment:

            • GenoMax
              replied
              Originally posted by Votinhkiem90 View Post
              thanks for help, What should I do? "/fs/szgenefinding/Glimmer3/bin/" directory not populated?
              I just realized that you compiled the software in a new location. So the directory you would want to check would be

              /home/tnt/Downloads/glimmer3.02/bin

                Leave a comment:

              • Votinhkiem90
                replied
                Originally posted by GenoMax View Post
                I do not see an error in the "make".

                Can you check "/fs/szgenefinding/Glimmer3/bin/" directory to see if it has been populated? You should now be able to run the original program as long as the executables are there in /fs/szgenefinding/Glimmer3/bin/ directory.
                thanks for help, What should I do? "/fs/szgenefinding/Glimmer3/bin/" directory not populated?

                  Leave a comment:

                • GenoMax
                  replied
                  I do not see an error in the "make".

                  Can you check "/fs/szgenefinding/Glimmer3/bin/" directory to see if it has been populated? You should now be able to run the original program as long as the executables are there in /fs/szgenefinding/Glimmer3/bin/ directory.

                    Leave a comment:

                  • Votinhkiem90
                    replied
                    Originally posted by GenoMax View Post
                    Did you compile the program after downloading the source?

                    Code:
                    /fs/szgenefinding/Glimmer3/bin/long-orfs: Command not found.
                    That seems to indicate that the script is unable to find the "long-orf" program that should be present in /bin after compilation.
                    Thank for help, I compiled but have an error.
                    * Make Target is all
                    ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Common all #####
                    make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Common'
                    make[1]: Nothing to be done for `all'.
                    make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Common'
                    ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/ICM all #####
                    make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/ICM'
                    make[1]: Nothing to be done for `all'.
                    make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/ICM'
                    ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Glimmer all #####
                    make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Glimmer'
                    make[1]: Nothing to be done for `all'.
                    make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Glimmer'
                    ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Util all #####
                    make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Util'
                    make[1]: Nothing to be done for `all'.
                    make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Util'
                    * Make Target is all
                    ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Common all #####
                    make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Common'
                    make[1]: Nothing to be done for `all'.
                    make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Common'
                    ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/ICM all #####
                    make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/ICM'
                    make[1]: Nothing to be done for `all'.
                    make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/ICM'
                    ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Glimmer all #####
                    make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Glimmer'
                    make[1]: Nothing to be done for `all'.
                    make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Glimmer'
                    ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Util all #####
                    make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Util'
                    make[1]: Nothing to be done for `all'.
                    make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Util'
                    * Make Target is all
                    ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Common all #####
                    make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Common'
                    make[1]: Nothing to be done for `all'.
                    make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Common'
                    ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/ICM all #####
                    make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/ICM'
                    make[1]: Nothing to be done for `all'.
                    make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/ICM'
                    ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Glimmer all #####
                    make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Glimmer'
                    make[1]: Nothing to be done for `all'.
                    make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Glimmer'
                    ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Util all #####
                    make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Util'
                    make[1]: Nothing to be done for `all'.
                    make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Util'
                    tnt@tnt:~/Downloads/glimmer3.02/src$ make
                    * Make Target is all
                    ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Common all #####
                    make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Common'
                    make[1]: Nothing to be done for `all'.
                    make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Common'
                    ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/ICM all #####
                    make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/ICM'
                    make[1]: Nothing to be done for `all'.
                    make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/ICM'
                    ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Glimmer all #####
                    make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Glimmer'
                    make[1]: Nothing to be done for `all'.
                    make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Glimmer'
                    ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Util all #####
                    make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Util'
                    make[1]: Nothing to be done for `all'.
                    make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Util'
                    * Make Target is all
                    ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Common all #####
                    make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Common'
                    make[1]: Nothing to be done for `all'.
                    make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Common'
                    ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/ICM all #####
                    make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/ICM'
                    make[1]: Nothing to be done for `all'.
                    make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/ICM'
                    ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Glimmer all #####
                    make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Glimmer'
                    make[1]: Nothing to be done for `all'.
                    make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Glimmer'
                    ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Util all #####
                    make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Util'
                    make[1]: Nothing to be done for `all'.
                    make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Util'
                    * Make Target is all
                    ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Common all #####
                    make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Common'
                    make[1]: Nothing to be done for `all'.
                    make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Common'
                    ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/ICM all #####
                    make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/ICM'
                    make[1]: Nothing to be done for `all'.
                    make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/ICM'
                    ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Glimmer all #####
                    make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Glimmer'
                    make[1]: Nothing to be done for `all'.
                    make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Glimmer'
                    ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Util all #####
                    make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Util'
                    make[1]: Nothing to be done for `all'.
                    make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Util'
                    tnt@tnt:~/Downloads/glimmer3.02/src$ cd ..
                    How to fix?

                      Leave a comment:

                    • GenoMax
                      replied
                      Originally posted by Votinhkiem90 View Post
                      tnt@tnt:~$ Downloads/glimmer3.02/sample-run/g3-from-scratch.csh auto_data_31/contigs.fa test
                      Step 1 of 4: Finding long orfs for training
                      /fs/szgenefinding/Glimmer3/bin/long-orfs: Command not found.
                      Failed to find long-orf training set

                      Did you compile the program after downloading the source?

                      Code:
                      /fs/szgenefinding/Glimmer3/bin/long-orfs: Command not found.
                      That seems to indicate that the script is unable to find the "long-orf" program that should be present in /bin after compilation.

                        Leave a comment:

                      • Votinhkiem90
                        started a topic How to run script (csh file) in Glimmer

                        How to run script (csh file) in Glimmer

                        tnt@tnt:~$ Downloads/glimmer3.02/sample-run/g3-from-scratch.csh auto_data_31/contigs.fa test
                        Step 1 of 4: Finding long orfs for training
                        /fs/szgenefinding/Glimmer3/bin/long-orfs: Command not found.
                        Failed to find long-orf training set

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