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Naama Menda nmenda

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@nmenda
nmenda / cxgnDBIC
Created September 14, 2009 14:53
my $dbh = CXGN::DB::InsertDBH->new( { dbhost=>$dbhost,
dbname=>$dbname,
dbschema => 'public',
} );
}
my $schema= Bio::Chado::Schema->connect( sub { $dbh->get_actual_dbh() }, );
@nmenda
nmenda / create_group_tables.sql
Created September 24, 2009 14:24
CREATE SCHEMA core;
CREATE TABLE core.group (
group_is serial NOT NULL PRIMARY KEY,
name varchar (255),
type integer REFERENCES public.cvterm(cvterm_id)
);
@nmenda
nmenda / gist:246576
Created December 1, 2009 19:47
Autoconfigured everything but 'urllist'.
Please call 'o conf init urllist' to configure your CPAN server(s) now!
Unknown config variable 'cpan_version_check'
commit: wrote '/home/naama/.cpan/CPAN/MyConfig.pm'
CPAN: File::HomeDir loaded ok (v0.64)
CPAN: LWP::UserAgent loaded ok (v5.813)
Fetching with LWP:
ftp://cpan.cs.utah.edu/pub/CPAN/authors/01mailrc.txt.gz
@nmenda
nmenda / gist:246872
Created December 2, 2009 02:24
Restarting web server: apache2
We failed to correctly shutdown apache, so we're now killing all running apache processes. This is almost certainly suboptimal, so please make sure your system is working as you'd expect now! (warning).
... waiting Syntax error on line 14 of /etc/apache2/sites-enabled/sgn:
Can't locate autodie.pm in @INC (@INC contains: /home/naama/cxgn/local-lib/lib/perl5 /home/naama/cxgn/local-lib/lib/perl5/i486-linux-gnu-thread-multi /home/naama/cxgn/cxgn-corelibs/lib /home/naama/cxgn/sgn/lib /usr/local/lib/site_perl /etc/perl /usr/local/lib/perl/5.10.0 /usr/local/share/perl/5.10.0 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10 . /etc/apache2) at /home/naama/cxgn/sgn/lib/SGN/Apache2/Startup.pm line 14.\nBEGIN failed--compilation aborted at /home/naama/cxgn/sgn/lib/SGN/Apache2/Startup.pm line 14.\nCompilation failed in require at /etc/apache2/sites-enabled/sgn line 18.\nBEGIN failed--compilation aborted\t(in cleanup) Can't locate autodie.pm in @INC (@INC contains: /ho
@nmenda
nmenda / sgn
Created December 2, 2009 14:01
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 $r object is not available. Set:\n\tPerlOptions +GlobalRequest\nin httpd.conf at /usr/local/lib/site_perl/CXGN/Apache/Request.pm line 118.\nCompilation failed in require at (eval 350) line 1.\nCompilation failed in require at /home/naama/cxgn/sgn/lib/SGN/Apache2/Startup.pm line 21.\nBEGIN failed--compilation aborted at /home/naama/cxgn/sgn/lib/SGN/Apache2/Startup.pm line 21.\nCompilation failed in require at /etc/apa
@nmenda
nmenda / gist:247338
Created December 2, 2009 16:51
# enable extended apache server status, which is sometimes useful for debugging
ExtendedStatus On
<VirtualHost *:80>
ServerName sgn.localhost.localdomain
PerlWarn On
PerlTaintCheck On
@nmenda
nmenda / DBIx::DBStag
Created December 9, 2009 17:59
naama@virtual:~/cxgn/sgn-tools$ cpan DBIx::DBStag
CPAN: Storable loaded ok (v2.18)
Going to read '/home/naama/.cpan/Metadata'
Database was generated on Thu, 12 Nov 2009 18:27:04 GMT
CPAN: YAML loaded ok (v0.70)
Going to read 188 yaml files from /home/naama/.cpan/build/
CPAN: Time::HiRes loaded ok (v1.9711)
DONE
Restored the state of none (in 2.1893 secs)
Running install for module 'DBIx::DBStag'
@nmenda
nmenda / libgd2
Created December 9, 2009 18:44
naama@virtual:~/cxgn/sgn$ sudo aptitude install libgd2-noxpm-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
Reading extended state information
Initializing package states... Done
Reading task descriptions... Done
The following packages are BROKEN:
libfreetype6-dev libgd2-noxpm-dev libpng12-dev
0 packages upgraded, 3 newly installed, 0 to remove and 0 not upgraded.
@nmenda
nmenda / XML::LibXML
Created December 9, 2009 18:58
CPAN.pm: Going to build P/PA/PAJAS/XML-LibXML-1.70.tar.gz
enable native perl UTF8
running xml2-config...
using fallback values for LIBS and INC
options:
LIBS='-L/usr/local/lib -L/usr/lib -lxml2 -lm'
INC='-I/usr/local/include -I/usr/include'
If this is wrong, Re-run as:
$ /usr/bin/perl Makefile.PL LIBS='-L/path/to/lib' INC='-I/path/to/include'
@nmenda
nmenda / find_mod_deps output
Created January 21, 2010 18:59
naama@virtual:~/cxgn/Phenome/trunk$ find_mod_deps.pl
for requires, grepping 72 files
sh: -c: line 0: syntax error near unexpected token `('
sh: -c: line 0: `grep -hP ^\s*(use|require|extends|with)\s+.+; lib/CXGN/Phenome.pm lib/CXGN/Phenome/LocusSynonym.pm lib/CXGN/Phenome/GenotypeRegion.pm lib/CXGN/Phenome/PopulationDbxref.pm lib/CXGN/Phenome/Main.pm lib/CXGN/Phenome/GenotypeExperiment.pm lib/CXGN/Phenome/Schema.pm lib/CXGN/Phenome/GenericGenePage.pm lib/CXGN/Phenome/Genotype.pm lib/CXGN/Phenome/Germplasm.pm lib/CXGN/Phenome/IndividualHistory.pm lib/CXGN/Phenome/Locus.pm lib/CXGN/Phenome/Allele.pm lib/CXGN/Phenome/LocusDbxref.pm lib/CXGN/Phenome/LocusGroup.pm lib/CXGN/Phenome/LocusgroupMember.pm lib/CXGN/Phenome/Population.pm lib/CXGN/Phenome/AlleleSynonym.pm lib/CXGN/Phenome/Locus2Locus.pm lib/CXGN/Phenome/Individual.pm lib/CXGN/Phenome/AlleleDbxref.pm lib/CXGN/Phenome/LocusMarker.pm lib/CXGN/Phenome/Locus/LocusRanking.pm lib/CXGN/Phenome/Locus/LocusUnigene.pm lib/CXGN/Phenome/Locus/LocusOwner.pm lib/CXGN/P