Difference between revisions of "Talk:GBrowse Install HOWTO"
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− | == | + | == 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. --[[User:DanBolser|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 | http://gmod.cvs.sourceforge.net/*checkout*/gmod/Generic-Genome-Browser/bin/gbrowse_netinstall.pl | ||
Line 14: | Line 14: | ||
− | + | : 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) | |
− | : | + | :: I found this error so far... Using the following command: |
+ | <pre>./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 *** | |
− | + | </pre> | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | == 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 --[[User:DanBolser|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? --[[User:DanBolser|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 ... | |
+ | |||
+ | <pre> | ||
+ | # 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 | ||
+ | </pre> | ||
− | + | --[[User:DanBolser|DanBolser]] 13:35, 16 January 2009 (UTC) |
Latest revision as of 13:35, 16 January 2009
Contents
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)