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Bioperl 1.6.1

by bilogical (Novice)
on Jan 15, 2010 at 05:53 UTC ( #817531=perlquestion: print w/replies, xml ) Need Help??
bilogical has asked for the wisdom of the Perl Monks concerning the following question:

I was trying to install BioPerl in windows using ppm. The latest version available is BioPerl 1.6.1 on When I tried to install it, a number of prerequisite modules were being installed too, which include Bioperl 1.4. Then an error message showed up:

“ERROR: File conflict for 'C:/Perl/html/bin/bp_aacomp.html'.The package BioPerl has already installed a file that package bioperl wants to install.”

It looks to me that BioPerl 1.6.1 had installed a file that bioperl 1.4 wanted to install again. I don’t know why bioperl 1.4 was one of the prerequisites for 1.6.1. If I just install 1.4, it will OK. But I need a newer version, because some modules (like Bio::Tools::HMM) is not included in 1.4.

I saw on internet that somebody had the same problem when he was trying to install BioPerl 1.5, but I didn't find the solution.

Anybody has a clue on that? Thank you for your time.

Replies are listed 'Best First'.
Re: Bioperl 1.6.1
by biohisham (Priest) on Jan 15, 2010 at 12:32 UTC
    With BioPerl, there are these repositories that you connect to, so you figure them out before you start installing BioPerl, and there are external modules too:
    • BioPerl-Release Candidates.
    • BioPerl Regular Releases.
    • Kobes.
    • Bribes.
    are the major repositories out there. It seems that there are a lot of dependencies involved and there are like 4 different ways to install BioPerl hence confusion erupts. Anyways, this link provides very nice instructions on how to connect these repositories via PPM GUI and PPM-Shell...

    After having installed BioPerl successfully, you might need to manage the PPM and enable/disable some of these repositories so as to maintain your ppm interface responsiveness, check PPM performs uneeded checks for a related discussion.

    Excellence is an Endeavor of Persistence. Chance Favors a Prepared Mind.

      Thanks for the reply.

      I followed up the instruction in the link you mentioned, and set up the repositories before installation. It is the BioPerl 1.6 version in the BioPerl Regular Releases depository that I was trying to install and found out the problem in the first post. I tried other ways to install as well, but various problems occurred.

        Having configured these repositories the same way mentioned in these links through PPM works reliably for me, then after that, running
        >ppm search BioPerl
        give me the following results "" corresponds to the BioPerl version you seek...Try starting a fresh iteration through these steps, delete the repositories and start afresh, then explain/mention the errors that you are getting...
Re: Bioperl 1.6.1
by Anonymous Monk on Jan 15, 2010 at 08:44 UTC
Re: Bioperl 1.6.1
by bilogical (Novice) on Jan 19, 2010 at 02:32 UTC

    Hi, The problem is solved now. The bioperl 1.4 version is from the Trouchelle repo, but 1.6 is in the Bioperl Regular Releases repo. When I added all the repo according to the bioperl wiki instruction, somehow 1.4 became a prerequisite for 1.6. But when I removed Trouchelle repo (so removed the 1.4 version), the installation proceeded without errors.

    Thank you all for the help and suggestions.



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