Difference between revisions of "Talk:GBrowse Install HOWTO"

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== ing? ==
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== Layout ==
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Aaaaaah.... --[[User:DanBolser|DanBolser]] 12:07, 28 October 2008 (UTC)
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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. --[[User:DanBolser|DanBolser]] 12:21, 28 October 2008 (UTC)
  
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== Question about gbrowse_netinstall.pl ==
 
  
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Soo... Looking at:
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== Question about gbrowse_netinstall.pl ==
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Looking at:
  
 
http://gmod.cvs.sourceforge.net/*checkout*/gmod/Generic-Genome-Browser/bin/gbrowse_netinstall.pl
 
http://gmod.cvs.sourceforge.net/*checkout*/gmod/Generic-Genome-Browser/bin/gbrowse_netinstall.pl
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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. --[[User:DanBolser|DanBolser]] 12:21, 28 October 2008 (UTC)
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: 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... --[[User:DanBolser|DanBolser]] 15:00, 28 October 2008 (UTC)
  
  
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: 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. To do that you may need to edit the file '~/.cpan/CPAN/MyConfig.pm' and set the value of PREFIX to somewhere sensible. There should be plenty of information on the internet describing how to set up cpan so you can install Perl modules as a non-root user. For some reason the '--install_param_str="PREFIX=~/build"' suggestion above does not seem to work, you need to configure cpan"
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:: I found this error so far... Using the following command:
  
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<pre>./gbrowse_netinstall.pl -d --install_param_str="PREFIX=~/test"
  
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Heh... part of MyConfig.pm looks like this:
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Manifying blib/lib/Bio/DB/Qual.pm -> blib/libdoc/Bio::DB::Qual.3pm
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
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ERROR: Can't create '/usr/bin'
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Do not have write permissions on '/usr/bin'
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
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  at /tmp/vbXS2SeDDc/bioperl-live/ModuleBuildBioperl.pm line 812
  
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[dbolser@cricket ~]$ grep "~" .cpan/CPAN/MyConfig.pm
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*** Installing Generic-Genome-Browser ***
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  'makepl_arg' => q[PREFIX=~/perl SITELIBEXP=~/perl/lib/perl5 LIB=~/perl/lib/perl5 INSTALLMAN1DIR=~/perl/share/man/man1 INSTALLMAN3DIR=~/perl/share/man/man3 INSTALLSITEMAN1DIR=~/perl/share/man/man1 INSTALLSITEMAN3DIR=~/perl/share/man/man3],
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</pre>
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[dbolser@cricket ~]$ grep bolser .cpan/CPAN/MyConfig.pm
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  'build_dir' => q[/homes/dbolser/.cpan/build],
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  'cpan_home' => q[/homes/dbolser/.cpan],
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  'histfile' => q[/homes/dbolser/.cpan/histfile],
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  'keep_source_where' => q[/homes/dbolser/.cpan/sources],
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If you ever happen to have done something like "sudo cpan", your in trouble. Make sure that nothing under ~/.cpan is owned by root, and configure cpan along the lines of the above (or using information on the internets).
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== CPAN as non-root? ==
  
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It seems that mostly gbrowse_netinstall.pl uses cpan, so lets see... --[[User:DanBolser|DanBolser]] 15:00, 28 October 2008 (UTC)
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See: http://sial.org/howto/perl/life-with-cpan/non-root/
  
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: More importantly see: http://search.cpan.org/search?query=local-lib --[[User:DanBolser|DanBolser]] 15:36, 14 January 2009 (UTC)
  
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::I wonder who I'm talking to... I found this error so far
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== Question about '''Optional Perl modules''' ==
  
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Manifying blib/lib/Bio/DB/Qual.pm -> blib/libdoc/Bio::DB::Qual.3pm
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Are the Bio:: Perl modules listed in this section not part of BioPerl? Why are these modules listed separately from BioPerl? --[[User:DanBolser|DanBolser]] 15:35, 14 January 2009 (UTC)
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
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ERROR: Can't create '/usr/bin'
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== GBrowse Quick Install ==
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Do not have write permissions on '/usr/bin'
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
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  at /tmp/vbXS2SeDDc/bioperl-live/ModuleBuildBioperl.pm line 812
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Assuming:
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* You have Apache installed and working in a way in which you understand ...
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   *** Installing Generic-Genome-Browser ***
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* You have Perl and BioPerl installed ...
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 +
<pre>
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# Local Perl modules:
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# /opt/perl/5.8.8/lib/perl5/
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# Local BioPerl modules:
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# /opt/bioperl/bioperl-live/lib/perl5/
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export PERL5LIB=/opt/perl/5.8.8/lib/perl5:/opt/bioperl/bioperl-live/lib/perl5
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perl Makefile.PL \
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  NOROOT=1 \
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   SELINUX=1 \
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  APACHE=$HOME/httpd \
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  GBROWSE_ROOT=gbrowse \
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  LIB=$HOME/perl5/lib/perl5
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## Aparently unused
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  BIN=$HOME/perl5/bin
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</pre>
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--[[User:DanBolser|DanBolser]] 13:35, 16 January 2009 (UTC)

Latest revision as of 13:35, 16 January 2009

Layout

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:

  • 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 \
  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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