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  • Need help for installing Bioperl on RedHat, CPAN shell problem

    Hi all,

    I am trying to install Bioperl on my RedHat fedora11 system, When i give command

    ~]$ perl -MCPAN -e shell

    it gives error msg

    Can't locate CPAN.pm in @INC (@INC contains: /usr/local/lib/perl5/site_perl/5.10.0/i386-linux-thread-multi /usr/local/lib/perl5/site_perl/5.10.0 /usr/lib/perl5/vendor_perl/5.10.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.10.0 /usr/lib/perl5/vendor_perl /usr/lib/perl5/5.10.0/i386-linux-thread-multi /usr/lib/perl5/5.10.0 /usr/lib/perl5/site_perl .).
    BEGIN failed--compilation aborted.

    i have tried this command

    # yum install perl-bioperl

    does it means bioperl is installed on my system?

  • #2
    Try

    Code:
    yum install perl-CPAN
    which will get CPAN installed.

    What message do you get with "yum install perl-bioperl"

    Comment


    • #3
      Originally posted by krobison View Post
      Try

      Code:
      yum install perl-CPAN
      which will get CPAN installed.

      What message do you get with "yum install perl-bioperl"
      Thanks for your reply,

      I have tried,

      Code:
      yum install perl-CPAN
      I am getting this ERROR,

      Transaction Check Error:

      Code:
      package perl-CPAN-2:1.61-94.EL3.i386 (which is newer than perl-CPAN-0:1.9205-82.fc11.i586) is already installed
      i didn't get any error message at the end of applying "yum install perl-bioperl".

      How to check whether BioPerl installed successfully or not?

      Comment


      • #4
        Firstly you're using a version of Fedora which is no longer supported, so you should think about upgrading to the latest version.

        Your immediate problem though is that you have installed an RPM for RHEL on a Fedora system, which means you have CPAN.pm installed, just in a location where your perl can't see it.

        The fix for your immediate problem is probably:

        yum remove perl-CPAN

        yum install perl-CPAN

        Which should install the correct version from your Fedora repositories.

        Comment


        • #5
          First Happy new year to all

          yum remove perl-CPAN

          yum install perl-CPAN

          It worked,

          Thanks for your precious inputs, krobison and simonandrews
          Last edited by ketan_bnf; 01-01-2011, 12:31 AM.

          Comment


          • #6
            I have installed activeperl in windows xp.
            through Perl Package Manager i have installed BioPerl repositories.
            but while trying to execute BioPerl program..
            #!/usr/bin/env perl
            use Bio::Seq;
            use Bio::SeqIO;

            # create a sequence object of some DNA
            my $seq = Bio::Seq->new(-id => 'testseq', -seq => 'CATGTAGATAG');

            # print out some details about it
            print "seq is ", $seq->length, " bases long\n";
            print "revcom seq is ", $seq->revcom->seq, "\n";

            # write it to a file in Fasta format
            my $out = Bio::SeqIO->new(-file => '>testseq.fsa', -format => 'Fasta');
            $out->write_seq($seq);

            the following error is coming

            Cant locate Bio/Seq.pm in @INC <INC contains : C:/Perl/site/lib C:/Perl/lib.> at C:\Perl\bin\Sequence.pl line1.
            BEGIN failed--compilation aborted at C:\Perl\bin\Sequence.pl line1.

            what is the problem here??

            How to identify whether BioPerl is installed or not???

            Please guide me....

            thanks & Regards

            Comment


            • #7
              Originally posted by shrujan View Post
              I have installed activeperl in windows xp.
              through Perl Package Manager i have installed BioPerl repositories.
              but while trying to execute BioPerl program..

              Cant locate Bio/Seq.pm in @INC <INC contains : C:/Perl/site/lib C:/Perl/lib.> at C:\Perl\bin\Sequence.pl line1.
              BEGIN failed--compilation aborted at C:\Perl\bin\Sequence.pl line1.
              If you've only installed the repositories you still need to install the BioPerl packages from those repositories. Try running:

              ppm install BioPerl

              ..from a command prompt.

              Comment


              • #8
                I have installed BioPerl in ppm after adding those repositories..but the issue is not yet resolved.

                Comment


                • #9
                  I just tried this on a windows machine and it all seemed to work OK. The BioPerl modules were all installed under C:/Perl/site/lib which was one of the directories listed in your @INC.

                  If you look in C:/Perl/site/lib is there a folder called Bio, and inside that is there a file called Seq.pm?

                  What output do you get if you run the following command at a command prompt?

                  ppm install BioPerl

                  Comment


                  • #10
                    this is coming...
                    Attached Files

                    Comment


                    • #11
                      ppm install failed is coming

                      Comment


                      • #12
                        it is showing that Math-Random-0.71 is not found...and it is showing ppm install failed.....

                        Comment


                        • #13
                          I can't see anything in the screenshot you posted as the resolution is so low. Math::Random is present in the standard ActiveState repositories so you should be able to install it from there. You didn't delete the standard repositories when you added in the ones for BioPerl did you?

                          Without seeing the exact error you're getting it's difficult to suggest what to do next - it's easier if you just copy and paste the text from the command window rather than putting in a screenshot (use the icon on the top left and select Mark to allow the selection of all text in the window, then press return to copy it).

                          Comment


                          • #14
                            ppm install failed: Don't know how to unpack http://bioperl.org/DIST/MSWin32-x86
                            -multi-thread-5.8/SVG-Graph-0.02.zip

                            this is coming when i tried to install BioPerl in command prompt...
                            Last edited by shrujan; 08-22-2012, 01:12 AM.

                            Comment


                            • #15
                              Originally posted by shrujan View Post
                              ppm install failed: Don't know how to unpack http://bioperl.org/DIST/MSWin32-x86
                              -multi-thread-5.8/SVG-Graph-0.02.zip

                              this is coming when i tried to install BioPerl in command prompt...
                              This thread on the activestate forums suggests that you're going to need a newer version of ppm as older versions didn't understand how to unpack zip files, only tar.gz. I used ppm v4.14 which came with ActivePerl 5.14.2 and that worked OK.

                              Comment

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