Talk:GBrowse Install HOWTO

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It would be good if the content of this page could be re-organized, as it seems to jump around a bit, and I think several sections could be placed on other (sub) pages. I'd do it... but I'm lazy, no wait, what I mean is that I don't want to start cutting and hacking away before I know what I am doing. --DanBolser 12:21, 28 October 2008 (UTC)

Question about

Looking at:*checkout*/gmod/Generic-Genome-Browser/bin/

I wonder if its possible to install 'non-root' using this PL? Seems like appropriate use of the '--install_param_str' could allow a non-root install via this package... would it be something like

perl --install_param_str PREFIX=~/build

At least part of the answer to this question is: "Yes, you can use as 'non-root', however, you should have your cpan configuration set up so that you can install Perl modules as a non-root user. It seems that mostly uses cpan, so lets see... --DanBolser 15:00, 28 October 2008 (UTC)

I found this error so far... Using the following command:
./ -d --install_param_str="PREFIX=~/test"

Manifying blib/lib/Bio/DB/ -> blib/libdoc/Bio::DB::Qual.3pm
ERROR: Can't create '/usr/bin'
Do not have write permissions on '/usr/bin'
  at /tmp/vbXS2SeDDc/bioperl-live/ line 812

*** Installing Generic-Genome-Browser ***

CPAN as non-root?


More importantly see: --DanBolser 15:36, 14 January 2009 (UTC)

Question about Optional Perl modules

Are the Bio:: Perl modules listed in this section not part of BioPerl? Why are these modules listed separately from BioPerl? --DanBolser 15:35, 14 January 2009 (UTC)

GBrowse Quick Install


  • You have Apache installed and working in a way in which you understand ...
  • You have Perl and BioPerl installed ...
# Local Perl modules:
# /opt/perl/5.8.8/lib/perl5/

# Local BioPerl modules:
# /opt/bioperl/bioperl-live/lib/perl5/

export PERL5LIB=/opt/perl/5.8.8/lib/perl5:/opt/bioperl/bioperl-live/lib/perl5

perl Makefile.PL \
  NOROOT=1 \
  APACHE=$HOME/httpd \
  GBROWSE_ROOT=gbrowse \

## Aparently unused

--DanBolser 13:35, 16 January 2009 (UTC)