Difference between revisions of "Talk:GBrowse Install HOWTO"

From GMOD
Jump to: navigation, search
Line 35: Line 35:
  
  
::I wonder who I'm talking to... I found this error so far
+
::I wonder who I'm talking to... I found this error so far... Using the following command:
 +
 
 +
::<pre>./gbrowse_netinstall.pl -d --install_param_str="PREFIX=~/test"</pre>
  
 
  Manifying blib/lib/Bio/DB/Qual.pm -> blib/libdoc/Bio::DB::Qual.3pm
 
  Manifying blib/lib/Bio/DB/Qual.pm -> blib/libdoc/Bio::DB::Qual.3pm
Line 43: Line 45:
 
  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
   at /tmp/vbXS2SeDDc/bioperl-live/ModuleBuildBioperl.pm line 812
 
   at /tmp/vbXS2SeDDc/bioperl-live/ModuleBuildBioperl.pm line 812
+
 
 
   *** Installing Generic-Genome-Browser ***
 
   *** Installing Generic-Genome-Browser ***

Revision as of 15:50, 28 October 2008

ing?

Aaaaaah.... --DanBolser 12:07, 28 October 2008 (UTC)

Question about gbrowse_netinstall.pl

Soo... 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


? 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)


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"


Heh... part of MyConfig.pm looks like this:

[dbolser@cricket ~]$ grep "~" .cpan/CPAN/MyConfig.pm
  '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],
[dbolser@cricket ~]$ grep bolser .cpan/CPAN/MyConfig.pm
  'build_dir' => q[/homes/dbolser/.cpan/build],
  'cpan_home' => q[/homes/dbolser/.cpan],
  'histfile' => q[/homes/dbolser/.cpan/histfile],
  'keep_source_where' => q[/homes/dbolser/.cpan/sources],

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).

It seems that mostly gbrowse_netinstall.pl uses cpan, so lets see... --DanBolser 15:00, 28 October 2008 (UTC)


I wonder who I'm talking to... 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 ***