This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
##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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
-- ================================================ | |
-- 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, |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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"; | |
}; |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
$rs->search( { 'observable.name' => $trait }, | |
{ join => { nd_experiment_stocks => [ nd_experiment => {'nd_experiment_phenotypes' => 'phenotype' => 'observable' } ] } } , | |
); |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
$cvterm->search_related( | |
'cvtermpath_objects', | |
undef, | |
{ | |
pathdistance => { '<' => 0 }, | |
} | |
) | |
->search_related('subject'); |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
naama@virtual sgn (topic/stock *%)$ 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) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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= |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
/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: |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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 | |
NewerOlder