rbuels

alias lr='find | grep -v .svn | grep -v ~$'
alias df='df -h'
alias s='cd ..'
alias ss='cd ../..'
alias sss='cd ../../..'

alias scp='scp -C'
alias wifi='sudo /root/bin/wifi'
alias ifconfig='sudo ifconfig'
alias iwconfig='sudo iwconfig'

rbuels

rob@banana perllib (master%)$ prove -I. -v   t/CXGN/Metadata/groups.t   
t/CXGN/Metadata/groups.t ..                                             
1..102                                                                  
ok 1 - use CXGN::Metadata::Schema;                                      
ok 2 - use CXGN::Metadata::Groups;                                      
ok 3 - use CXGN::Metadata::Metadbdata;                                  
ok 4 - use CXGN::Metadata::Dbiref;                                      
ok 5 - BASIC SET/GET FUNCTION for group_description test                
ok 6 - BASIC SET/GET FUNCTION for group_id test                         
ok 7 - BASIC SET/GET FUNCTION for group_name test                       

rbuels

BEGIN {
   package Foo::Schema::MyTable;
   .... #define the dbic stuff

   package Foo::Schema;
   __PACKAGE__->load_classes('Foo::Table');
}

BEGIN {
   package Bar::Schema::MyOtherTable;

rbuels

  my $merged_schema = CXGN::DB::DBICFactory
                        ->merge_schemas( 'Bio::Chado::Schema',
                                         'SGN::Schema',
                                         { search_path => ['public','sgn'],
                                         },
                                       );
sub merge_schema {
    # get args
    my $class = shift;
    my $options = pop;

rbuels

#!/bin/sh

PSQL="sudo -u postgres psql cxgn"

set -e
sudo echo;

#ssh db.sgn.cornell.edu  pg_dump --clean --schema-only --schema genomic --host localhost --user postgres cxgn | $PSQL

sudo echo;

rbuels

use strict;
use warnings;
use inc::Module::Install;
BEGIN {
    push @INC, sub {
        warn "Module::Install: missing configure_requires dependency:\n";
    };
}
use ExtUtils::Depends;
use B::Hooks::OP::Check;

rbuels

Index: lib/Module/Install.pm      
===================================================================
--- lib/Module/Install.pm       (revision 9914)                    
+++ lib/Module/Install.pm       (working copy)                     
@@ -116,9 +116,14 @@                                               
 $^H |= strict::bits(qw(refs subs vars));                          
                                                                   
                                                                   
+# add a warning to the end of @INC, so that if a module load failure
+# happens in a Makefile.PL, add a helpful warning                   

rbuels

=head1 NAME
 
CXGN::Biosource::ProtocolTool
a class to manipulate a biosource tool data.
 
Version: 0.1
 
=head1 SYNOPSIS
 
  use CXGN::Biosource::ProtocolTool;

rbuels

#!/usr/bin/perl

my $new_seq = Bio::Seq::RichSeq->new();

my $searchio = Bio::SearchIO->new( -format => 'blastxml',
                                   -file   => 'blastout.xml' );
while ( my $result = $searchio->next_result() ) {
    while( my $hit = $result->next_hit ) {
        # process the Bio::Search::Hit::HitI object
        while( my $hsp = $hit->next_hsp ) {

rbuels

Restarting web server: apache2Syntax error on line 14 of /etc/apache2/sites-enabled/sgn:
Global $r object is not available. Set:\n\tPerlOptions +GlobalRequest\nin httpd.conf at /usr/local/lib/site_perl/CXGN/Apache/Request.pm line 118.\nCompilation failed in require at (eval 350) line 1.\nCompilation failed in require at /home/naama/cxgn/sgn/lib/SGN/Apache2/Startup.pm line 21.\nBEGIN failed--compilation aborted at /home/naama/cxgn/sgn/lib/SGN/Apache2/Startup.pm line 21.\nCompilation failed in require at /etc/apache2/sites-enabled/sgn line 18.\nBEGIN failed--compilation aborted\t(in cleanup) Global $r object is not available. Set:\n\tPerlOptions +GlobalRequest\nin httpd.conf at /usr/local/lib/site_perl/CXGN/Apache/Request.pm line 118.\nCompilation failed in require at (eval 350) line 1.\nCompilation failed in require at /home/naama/cxgn/sgn/lib/SGN/Apache2/Startup.pm line 21.\nBEGIN failed--compilation aborted at /home/naama/cxgn/sgn/lib/SGN/Apache2/Startup.pm line 21.\nCompilation failed in require at /etc/apa