nmenda

##Shell script for running tophat2 and cuffdiff
##Place in /home/bioinfo/Data/test_RNAseq to use

#Step 1: run index the reference fasta file for faster match searching
bowtie2-build bwt2_index/SL2.40ch04.fa bwt2_index/SL2.40ch04

#Step 2: run tophat2 on first breaker fastq file
tophat2 -o fastq/breaker/SRR404334_ch4_thout --no-novel-juncs --no-coverage-search bwt2_index/SL2.40ch04 fastq/breaker/SRR404334_ch4.fastq

#Step 3: run tophat2 on second breaker fastq file

nmenda

-- ================================================
-- TABLE: genotypeprop
-- ================================================
create table genotypeprop (
    genotypeprop_id serial not null,
    primary key (genotypeprop_id),
    genotype_id int not null,
    foreign key (genotype_id) references genotype (genotype_id) on delete cascade INITIALLY DEFERRED,
    type_id int not null,
    foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,

nmenda

try {
    $schema->txn_do($coderef);
    if (!$opt_t) { print "Transaction succeeded! Commiting stocks and their properties! \n\n"; }
} catch {
    # Transaction failed
      die "An error occured! Rolling back  and reseting database sequences!" . $_ . "\n";
};

nmenda

 $rs->search( { 'observable.name' => $trait },
                     { join => { nd_experiment_stocks => [ nd_experiment => {'nd_experiment_phenotypes' => 'phenotype' => 'observable' } ] } } ,
            );

nmenda

08:17:04.386 INFO - Allocated session 529f4681d7044ea58296b22dfd1aaefe for http://sgn-devel.localhost.localdomain:3000, launching...
08:17:04.538 INFO - Preparing Firefox profile...
08:17:07.675 INFO - Launching Firefox...
08:17:11.800 INFO - Got result: OK,529f4681d7044ea58296b22dfd1aaefe on session 529f4681d7044ea58296b22dfd1aaefe
08:17:11.806 INFO - Command request: setTimeout[60, ] on session 529f4681d7044ea58296b22dfd1aaefe
08:17:11.868 INFO - Got result: OK on session 529f4681d7044ea58296b22dfd1aaefe
08:17:11.873 INFO - Command request: open[/content/sgn_data.pl, ] on session 529f4681d7044ea58296b22dfd1aaefe
08:17:11.953 INFO - Got result: Timed out after 60ms on session 529f4681d7044ea58296b22dfd1aaefe
08:17:11.958 INFO - Command request: mouseOver[id=Nicotiana attenuata, ] on session 529f4681d7044ea58296b22dfd1aaefe
08:17:11.988 INFO - Got result: ERROR: Element id=Nicotiana attenuata not found on session 529f4681d7044ea58296b22dfd1aaefe

nmenda

 $cvterm->search_related(
            'cvtermpath_objects',
            undef,
            {
                pathdistance => { '<' =>  0 },
            }
           )
            ->search_related('subject');

nmenda

naama@virtual sgn (topic/stock *%)$ git status
# On branch topic/stock
# Changed but not updated:
#   (use "git add <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#
#	modified:   lib/SGN.pm
#
# Untracked files:
#   (use "git add <file>..." to include in what will be committed)

nmenda

Caught exception in SGN::View::Mason->process "Can't find component for path /cgi/CGI_phenome_2fassign_owner_2epl.mas at /home/naama/cxgn/local-lib/lib/perl5/Catalyst/View/HTML/Mason.pm line 204
	Catalyst::View::HTML::Mason::fetch_comp('SGN::View::Mason=HASH(0xb7b94328)', 'cgi/CGI_phenome_2fassign_owner_2epl.mas') called at /home/naama/cxgn/local-lib/lib/perl5/Catalyst/View/HTML/Mason.pm line 167
	Catalyst::View::HTML::Mason::__ANON__() called at /home/naama/cxgn/local-lib/lib/perl5/Try/Tiny.pm line 76
	eval {...} called at /home/naama/cxgn/local-lib/lib/perl5/Try/Tiny.pm line 67
	Try::Tiny::try('CODE(0x1435afd0)', 'Try::Tiny::Catch=REF(0x1435a220)') called at /home/naama/cxgn/local-lib/lib/perl5/Catalyst/View/HTML/Mason.pm line 173
	Catalyst::View::HTML::Mason::render('SGN::View::Mason=HASH(0xb7b94328)', 'SGN=HASH(0x1430e0f8)', 'cgi/CGI_phenome_2fassign_owner_2epl.mas') called at /home/naama/cxgn/local-lib/lib/perl5/Catalyst/View/HTML/Mason.pm line 182
	Catalyst::View::HTML::Mason::process('SGN::View::Mason=

nmenda

/home/naama/cxgn/ITAG/lib:/home/naama/cxgn/tomato_genome/lib:/home/naama/cxgn/Cview/lib:/home/naama/gmod/trunk/chado/lib:/home/naama/github/Bio-Chado-Schema/lib:/home/naama/cxgn/Phenome/lib:/home/naama/cxgn/cxgn-corelibs/lib:/home/naama/cxgn/local-lib/lib/perl5:/home/naama/cxgn/local-lib/lib/perl5/i486-linux-gnu-thread-multi:

nmenda

Catalyst::Action::RenderView uses NEXT, which is deprecated. Please see the Class::C3::Adopt::NEXT documentation for details. NEXT used  at /usr/share/perl5/Catalyst/Action/RenderView.pm line 18
[info] *** Request 1 (0.008/s) [27675] [Fri Aug 27 13:38:58 2010] ***
[debug] "GET" request for "sequencing/sol100.pl" from "192.168.3.1"
[debug] Path is "sequencing/sol100.pl"
[debug] Response Code: unknown; Content-Type: text/html; Content-Length: 136
[info] Request took 0.130631s (7.655/s)
.------------------------------------------------------------+-----------.
| Action                                                     | Time      |
+------------------------------------------------------------+-----------+
| /auto                                                      | 0.001597s |