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  • unable to use Bio::Seq in perl

    Hi Forum Members,
    OS: Ubuntu 12.04
    Perl: 5.14
    I am facing issues working on Bio:erl
    Steps I followed:
    1) CPAN
    2) cpan>d /bioperl/
    3) cpan>install C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz


    I can see Bio folder in /home/.cpan/BioPerl-1.6.1/Bio
    But this is not available at /usr/bin

    Please help me.
    Bioinformaticscally calm

  • #2
    Why don't you just use the ubuntu repos?

    sudo apt-get install bioperl
    should do the job ..

    Comment


    • #3
      Originally posted by sklages View Post
      Why don't you just use the ubuntu repos?
      should do the job ..
      I need to get it installed by cpan.
      Thanks you for letting me know that way.
      Bioinformaticscally calm

      Comment


      • #4
        Why?

        Nevertheless, cpan should install modules somewhere in @INC. /usr/bin shouldn't be considered.

        Have you installed all dependencies mentioned in the url you posted, depending on what you need, http://www.bioperl.org/wiki/BioPerl_Dependencies

        Have you had any failed tests during installation? If so, the install process probably has not finished. If you are not worried about the failed tests (check!), then you can run installation via "force install C/CJ/CJFIELDS/BioPerl-1.6.0.tar.gz".

        Comment


        • #5
          When I install, I can see messages:
          'couldn't establish connection to database. Aborting tests'
          Unfortunately, nothing is being added to my @INC by cpan.

          Originally posted by sklages View Post
          Why?

          Nevertheless, cpan should install modules somewhere in @INC. /usr/bin shouldn't be considered.

          Have you installed all dependencies mentioned in the url you posted, depending on what you need, http://www.bioperl.org/wiki/BioPerl_Dependencies

          Have you had any failed tests during installation? If so, the install process probably has not finished. If you are not worried about the failed tests (check!), then you can run installation via "force install C/CJ/CJFIELDS/BioPerl-1.6.0.tar.gz".
          Bioinformaticscally calm

          Comment


          • #6
            @sklages
            Woah, using force, I can now use Bio::Seq
            Thanks much!
            Bioinformaticscally calm

            Comment

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