Hi Darwin,
I just discovered this problem yesterday;
Bio::DB::SeqFeature::Store::Alias is supposed to be provided by the
GBrowse 2.49 package, but it was left out of the manifest, so it
didn't get included in the package. Probably the easiest way to fix
this is to get Alias.pm:
https://raw.github.com/GMOD/GBrowse/master/lib/Bio/DB/SeqFeature/Store/Alias.pmand place it in your @INC (in the Store directory under
Bio/DB/SeqFeature). Once that is in place, you should be able to
install GBrowse 2.49 from cpan.
Scott
On Fri, Apr 27, 2012 at 8:04 PM, Darwin Sorento Dichmann
<
[hidden email]> wrote:
> Greetings,
>
> In an attempt to update my local Gbrowse2.17 to the newest version I destroyed it. I believe I updated all prerequisites prior to updating and had no serious warnings during the install.
>
> It seems to fail because it can't find Bio/DB/SeqFeature/Store/Alias.pm in @INC. I get this error from apache2, which I think is the problem:
> ---
> Can't locate Bio/DB/SeqFeature/Store/Alias.pm in @INC (@INC contains: /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0 .) at /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser2/DataSource.pm line 10, <DATA> line 192., referer:
http://localhost/cgi-bin/gb2/gbrowse/frog7/?source=frog7> ---
>
> I added this <export PERL5LIB=/Library/Perl/5.10.0> to my .bash_profile to include the folders that contain Bio/DB/SeqFeature/Store, but it didn't solve anything. I confess to not understanding this alias very well. Do I need to add a symbolic link somewhere?
>
> I had no problems with my previous version, so I am surprised that I ran into this problem.
>
> Any help is greatly appreciated,
> Darwin
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Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (
http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
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