TARO Developer Documentation / CGI scripts

Overview

TARO web interface is predominantly built using dynamically generated pages. Scripting language is Perl, technology CGI. Scripts visualize the content of the database. Scripts are completely independent (do not have references to each other in the code), however the pages generated by one script can have references to other. Only one script starts a calculation pipeline which is a targpipe_save.pl The command is:

source /gridware/sge/default/common/settings.sh &&
qsub -R y -o /fc_gpfs/gjb_lab/www-refine/pipeline_newclus/TO$n/job_logs
-e /fc_gpfs/gjb_lab/www-refine/pipeline_newclus/TO$n/job_logs -q 64bit-pri.q -N TarO -l h_vmem=9000M -l mem_used=12000M -l mem_free=3000M -l qname=64bit-pri.q -l www_refine=1 -S
/usr/bin/perl
/homes/www-refine/SSPF_TO1/TarO_newclus/TO_masterpipe_onNewClus.pl
'/usr/bin/perl /homes/www-refine/SSPF_TO1/TarO_newclus/TarO_indevel.pl -i
/fc_gpfs/gjb_lab/www-refine/pipeline_newclus/TO$n/TO$n.fasta -o
/fc_gpfs/gjb_lab/www-refine/pipeline_newclus/TO$n -j
/homes/www-refine/NOBACK/pipeline_results/raw_pipe_out_newclus -t
/local/gjb_lab/refine/tmp/refine -p
/homes/www-refine/SSPF_TO1/TarO_newclus -b $msaNum'";

TARO web interface overview
Script	Script description	References from code	References from generated page
targpipe_home.pl (CGI script) Accepted parameters: None or logout=true or guestlogin=guest or login=username passw=user password	This script generates TARO main page (with and without user credentials) which lists the queries of a user	global.pm:dopage() TOUtils.lib:calcStyleClass() Connects to DB	Standard header references: www.compbio.dundee.ac.uk itself TarO_help.html targpipe_input.pl Also: Anchored TarO_help.html www.compbio.dundee.ac.uk targpipe_display_query_seqs.pl?query=661 &funcdesc=Another%20test%20query
TarO_help.html	Static HTML help page
targpipe_input.pl Accepted parameters: none	Generate input fields for query submission	global.pm:dopage()	Standard header references ./example_fasta.pl POST to /targpipe_save.pl
targpipe_save.pl Accepted parameters: function fastafile msaNum or instead of fastafile fastatextarea	Confirms the submission, validate input, displays user input data and the query ID. AmbNNN input is Detailed break down of functions: Makes directory "mkdir -p /fc_gpfs/gjb_lab/www-refine/pipeline_newclus/TO<QUERY_ID>/job_logs" Writes FASTA file ">/fc_gpfs/gjb_lab/www-refine/pipeline_newclus/TO<QUERY_ID>/TO<QUERY_ID>.fasta" Insert new query in the pipe_QUERY table TARO DB Inserts query sequence to pipe_USER_SEQUENCE table Inserts calculation steps into PIPE_QUERY_STEP_STATUS table Insert query_id, 1 INTO PIPE_CAN_DISPLAY_QUERY (apparently without this query will not be displayed!) Submits a new job to the cluster	global.pm:dopage() #SSPF_TO1/TarO_newclus/upload/update_query_display.pl	Standard header references POST to /targpipe_home.pl (could do with GET no parameters seems to be taken into account)
targpipe_display_query_seqs.pl Accepted parameters: query=QUERYID funcdesc=DESCRIPTION where funcdesc is pass through parameter added to the action links on the page	Identify user Display user's query based on the query ID supplied	TarO_indevel::lookup_user() global.pm:dopage() TOUtils.lib:calcStyleClass()	Standard header references targpipe_popup_seq.pl targpipe_display.pl targpipe_display_homologs.pl targpipe_popup_annotation.pl targpipe_popup_pdb.pl targpipe_rps_blast.pl
targpipe_display.pl Accepted parameters: query=QUERYID funcdesc=DESCRIPTION sequence_ID	Display orthologues of the query sequence /htdocs/download/ortho$query_ID.tab /htdocs/download/ortho$query_ID.html	global.pm:dopage() TarO_indevel::lookup_user() TOUtils.lib:calcStyleClass()	Other links are as above (similar to targpipe_display_query_seqs.pl)
targpipe_rps_blast.pl Accepted parameters: query_id seq_id funcdesc	Displays RPS-BLAST Results	Does not use standard header function (global.pm:dopage()) TOUtils.lib:calcStyleClass()	TO_info.html - does not exist TarO_help.html
targpipe_popup_annotation.pl Accepted parameters: query_id seq_id funcdesc	Display annotations depending on the parameter passes (e.g. NetNglyc)	TOUtils.lib:calcStyleClass()
targpipe_popup_pdb.pl Accepted parameters: query_id seq_id	Displays PDB BLASTP or PSI BLAST Top Hits		TO_info.html - does not exist TarO_help.html
targpipe_display_homologs.pl Accepted parameters: query sequence_ID funcdesc	Output: /htdocs/download/homol$query_ID.tab /htdocs/download/homol$query_ID.html	global.pm:dopage() TarO_indevel::lookup_user() TOUtils.lib:calcStyleClass()
targpipe_popup_seq.pl Accepted parameters: query_id seq_id funcdesc	Display query sequence in the popup

Functions description
Function (package:name)	Function description
global.pm:dopage()	Generate header and footer for the page insert body generated elsewhere
TOUtils.lib:calcStyleClass()	vary CSS style for each row of the table
SSPF_TO1/TarO_newclus/upload/update_query_display.pl	Updates the pipe_can_display_QUERY table with query id and status
various:FormatDispNum<2,4,5,6>	Format the number to be displayed on a web page.
various:CreateLink(s)	Make a link to a specific resource, some incarnations accept "type" parameters
various:FormatDispText	Prevents null to be displayed on a web page

Taro Pipeline Calculation Steps
Number	Step Name
1	Orthologue searching (BLAST COG)
2	Homologue searching (PSIBLAST UniRef100)
(3)	Search known structures (BLAST ASTRAL) NOT IN USE
4	Search Structural Genomics targets (BLAST TargetDB)
5	Protein Disorder Prediction (Globplot & Disembl)
(6)	Infer InterPro annotation NOT IN USE
7	RPSBLAST Search CDD, Pfam, COG, KOG & SMART
8	Secondary Structure Prediction (Jpred)
9	Calculate elementary chemical properties
10	Predict transmembrane regions (TMHMM2)
11	Predict signal peptide (SIGNALP)
12	Multiple sequence alignment (MUSCLE)
13	Search known structures (PSIBLAST PDB)
14	Glycosylation site prediction (NetNglyc, NetOglyc)
15	Phosphorylation site prediction (NetPhos)
16	Protein Disorder Prediction (RONN)
17	Protein Crystallisation Propensity prediction (ParCrys & OB-Score)

Taro Pipeline Calculation Status
Status
Started
Results Available
Error (availble only for Jpred prediction)
Not Implemented (NOT USED)
Calculation Completed