solgenomics

psql -AX -f t/sql/plperl6.sql
1..9
ok 1 - Return an integer from PL/Perl6
ok 2 - Return nothing from PL/Perl6
ok 3 - Return a float from PL/Perl6
ok 4 - Return a varchar from PL/Perl6
ok 5 - Use a single quote in a PL/Perl6 procedure
ok 6 - Calculate the sum of all Fibonacci numbers <= 100
not ok 7 - We can return an argument unchanged
# Failed test 7: "We can return an argument unchanged"

solgenomics

rob@eggplant:~/pipelines/itag$ sudo -u itagpipeline ./run.sh ITAG/bin/itag_batch.pl -L -d ~/itagpipeline run 7 sgn_unige\
n
es
running sgn_unigenes in batch 7
CXGN::Tools::Run: WARNING: cluster queue contains more than 2000 (max_cluster_jobs) jobs, throttling job submissions
 at /data/shared/home/rob/pipelines/itag/ITAG/lib/CXGN/ITAG/Pipeline/Analysis.pm line 838
qstat: Unknown Job Id 417939.eggplant.cluster.sgn
CXGN::Tools::Run: cluster job id: 417939.eggplant.cluster.sgn
CXGN::Tools::Run: start time: 2010-05-27 06:22:39 EDT
CXGN::Tools::Run: error time: 2010-05-27 06:25:53 EDT

solgenomics

rob@blade2:~/pipelines/itag$ sudo -u itagpipeline ./run.sh ITAG/bin/itag_batch.pl -L -d ~/itagpipeline run 7 sgn_unigenes
Password:
running sgn_unigenes in batch 7
CXGN::Tools::Run: WARNING: cluster queue contains more than 2000 (max_cluster_jobs) jobs, throttling job submissions
 at /data/shared/home/rob/pipelines/itag/ITAG/lib/CXGN/ITAG/Pipeline/Analysis.pm line 838
CXGN::Tools::Run error running `qsub`: qsub: Invalid credential
CXGN::Tools::Run retrying cluster job submission.
CXGN::Tools::Run: cluster job id: 406351.eggplant.cluster.sgn
CXGN::Tools::Run: start time: 2010-05-19 00:05:27 EDT
CXGN::Tools::Run: error time: 2010-05-19 00:08:06 EDT

solgenomics

rob@blade2:~/pipelines/itag$ sudo -u itagpipeline ./run.sh ITAG/bin/itag_batch.pl -L -d ~/itagpipeline run 7 sgn_unigenes
running sgn_unigenes in batch 7
CXGN::Tools::Run: WARNING: cluster queue contains more than 2000 (max_cluster_jobs) jobs, throttling job submissions
 at /data/shared/home/rob/pipelines/itag/ITAG/lib/CXGN/ITAG/Pipeline/Analysis.pm line 838
CXGN::Tools::Run: cluster job id: 409069.eggplant.cluster.sgn
CXGN::Tools::Run: start time: 2010-05-20 00:18:19 EDT
CXGN::Tools::Run: error time: 2010-05-20 00:26:27 EDT
CXGN::Tools::Run: command failed: 'itag_wrapper perl -MCXGN::ITAG::Pipeline::Analysis::sgn_unigenes -e CXGN::ITAG::Pipeline::An
alysis::sgn_unigenes->run_gth('scaffold760','/data/shared/tomato_genome/itagpipeline/itag/pipe001/batch007/seq/scaffold760.seq.
vecscreened.itag001.batch007.v1.fasta','/data/prod/tmp/itag-analysis-sgn_unigenes-DlPM9v/scaffold760/xml','/data/prod/tmp/itag-

solgenomics

rob@banana sgn (master$)$ a2restart; prove `perl -E 'print join " ", map "-I $_", @ARGV' ../*/lib` -lrv t/bulk.t                                                                                      
 * Restarting web server apache2                                                                   apache2: Could not reliably determine the server's fully qualified domain name, using 127.0.1.1 for ServerName
apache2: Could not reliably determine the server's fully qualified domain name, using 127.0.1.1 for ServerName
                                                                                            [ OK ]
t/bulk.t ..
ok 1 - GET http://sgn.localhost.localdomain/bulk/input.pl?mode=unigene
ok 2 - Content contains "Download unigene information"
ok 3 - Form submit test
ok 4 - Result page title check
ok 5 - Result check 1

solgenomics

rob@banana cxgn-corelibs (master$)$ sudo parted /dev/sda
GNU Parted 1.8.8
Using /dev/sda
Welcome to GNU Parted! Type 'help' to view a list of commands.
(parted) p
Model: ATA INTEL SSDSA2MH08 (scsi)
Disk /dev/sda: 80.0GB
Sector size (logical/physical): 512B/512B
Partition Table: msdos

solgenomics

running sgn_unigenes in batch 7
CXGN::Tools::Run: cluster job id: 392852.eggplant.cluster.sgn
CXGN::Tools::Run: date: 2010-05-15 04:11:44 EDT
CXGN::Tools::Run: command failed: 'itag_wrapper perl -MCXGN::ITAG::Pipeline::Analysis::sgn_unigenes -e CXGN::ITA
G::Pipeline::Analysis::sgn_unigenes->run_gth('scaffold174','/data/shared/tomato_genome/itagpipeline/itag/pipe001
/batch007/seq/scaffold174.seq.vecscreened.itag001.batch007.v1.fasta','/data/prod/tmp/itag-analysis-sgn_unigenes-
2JsDQD/scaffold174/xml','/data/prod/tmp/itag-analysis-sgn_unigenes-2JsDQD/scaffold174/gff3')'
CXGN::Tools::Run: Command failed on host 'shiv4', user 'itagpipeline', with $?=9, exit value 0, signal KILL (9), $r=5677, $!='' (string could be spurious)
CXGN::Tools::Run: last few lines of stdout:
CXGN::Tools::Run: last few lines of stderr:

solgenomics

#!/usr/bin/env perl                                                       
use strict;                                                               
use warnings;                                                             

use CGI;
use JSON::Any;
use Mail::Sendmail;
use Tie::Function; 

use DateTime::Format::ISO8601;

solgenomics

(datura)(~/git/sgn master$ )$ git rebase git-svn
First, rewinding head to replay your work on top of it...
Applying: Add more tests to t/bulk.t
Applying: Add more tests for downloading bulk data to t/bulk.t
Applying: Add tests for microarray and clone_search modes on /bulk/input.pl
Applying: Add test for bulk bac_end
Applying: added markup_string.mas, which displays an arbitrary string formatted with Text.Markup
Using index info to reconstruct a base tree...
Falling back to patching base and 3-way merge...
Auto-merging mason/util/markup_string.mas

solgenomics

# enable extended apache server status, which is sometimes useful for debugging
ExtendedStatus On

<VirtualHost *:80>

    ServerName sgn.localhost.localdomain

    PerlWarn On
    PerlTaintCheck On