Bioperl 1.6.1

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 http://bioperl.org/DIST. 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.

Comment on Bioperl 1.6.1

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.	[reply] [d/l]
Re^2: Bioperl 1.6.1 by bilogical (Novice) on Jan 18, 2010 at 02:39 UTC
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.	[reply]
Re^3: Bioperl 1.6.1 by Anonymous Monk on Jan 18, 2010 at 11:58 UTC
Having configured these repositories the same way mentioned in these links through PPM works reliably for me, then after that, running `>ppm search BioPerl` [download] give me the following results " Read more... Link Title Here (47 kB) " 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...	[reply] [d/l] [select]
Re: Bioperl 1.6.1 by Anonymous Monk on Jan 15, 2010 at 08:44 UTC
Some ideas report the problem to repository operator and maybe ActiveState A Guide to Installing Modules http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz or `cpan CJFIELDS/BioPerl-1.6.1` or `cpanp i CJFIELDS/BioPerl-1.6.1`	[reply] [d/l] [select]
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. Best, GH	[reply]