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Talk%253AGBrowse 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 gbrowse_netinstall.pl

Looking at:

http://gmod.cvs.sourceforge.net/checkout/gmod/Generic-Genome-Browser/bin/gbrowse_netinstall.pl

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 gbrowse_netinstall.pl --install_param_str PREFIX=~/build

At least part of the answer to this question is: “Yes, you can use gbrowse_netinstall.pl 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 gbrowse_netinstall.pl uses cpan, so lets see… –DanBolser 15:00, 28 October 2008 (UTC)

I found this error so far… Using the following command:

./gbrowse_netinstall.pl -d --install_param_str="PREFIX=~/test"

Manifying blib/lib/Bio/DB/Qual.pm -> 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/ModuleBuildBioperl.pm line 812

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

CPAN as non-root?

See: http://sial.org/howto/perl/life-with-cpan/non-root/

More importantly see: http://search.cpan.org/search?query=local-lib –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

Assuming:

# 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 \
  SELINUX=1 \
  APACHE=$HOME/httpd \
  GBROWSE_ROOT=gbrowse \
  LIB=$HOME/perl5/lib/perl5

## Aparently unused
  BIN=$HOME/perl5/bin

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

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