Workflow Entry: Blast against ENSEMBLE Danio_rerio_Genome

Created at: 15/10/08 @ 08:43:51 Last updated: 15/10/08 @ 09:21:35

Version 1 (of 1)

Version created on: 15/10/08 @ 08:43:51 by: Wassinki | Revision comments Expand

Last edited on: 15/10/08 @ 09:21:36 by: Wassinki

Title: Blast against ENSEMBLE Danio_rerio_Genome

Type: Taverna 1

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Description

This workflow invokes the blast service provided at www.bioinformatics.nl, written by Pieter Neerincx. The workflow takes as input a database name (Danio_rerio_Genome for Zebra Fish for example) and a set of sequences in fasta format. The blast service is invoked (using polling) and the result is a tab separated blast report.

To run this workflow, a certificate to access www.bioinformatics.nl needs to installed (Some services use an SSL connection). Look at the link below how to install this certificate.

http://www.myexperiment.org/files/148

Download

Download Workflow File/Package (SCUFL)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Launch in Taverna

Note: you need to have both the WHIP Launcher and the Taverna myExperiment/WHIP plugin installed on your machine for this to work. See here for information.

Option 2:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/530/download?version=1
[ More Info Expand ]

Workflow Components

Inputs (2)

Name	Description
Sequences
DataBaseName

Processors (13)

Name	Type	Description
Flatten_urls	local
DownloadURLWithBasicAuth	beanshell	This Beanshell downloads a file to disk. The standard download local Java widgets don't handle URLs with HTTP(S) Basic Authentication, but this Beanshell can. When a webserver uses BasicAuth, a login and password can be coded as part of the URL using the following syntax: http(s)://login:password@www.some.website/my/great/tool/result.xml. This beanshel extracts the login and password from the URL and supplies them automatically to the webserver. This prevents Taverna from showing popup dialogs requesting the login and password from the user as this will be problematic for large workflows. Please note that the path where the downloaded file will be stored must be an absolute path to a folder ended with a slash. (Slash backward on Windows or a slash forward on Linux/Unix/Mac OS X.) The filename for the result is automatically extracted from the URL.
Parse_Moby_Data_URL	biomobyparser	Processor to parse the datatype URL
Program	biomobyobject	A generic program object.
MobyBlast_submit	biomobywsdl	Submit a BLAST Job and retrieve a Job ID. Use this Job ID with the MobyBlast_poll service from the same service provider to check the status of your job.Use this Job ID with the MobyBlast_retrieve service from the same service provider to fetch the results.
DataBase	biomobyobject	A database object.
Email	biomobyobject	An e-mail address object.
String	biomobyobject	a string
User	biomobyobject	A generic user object.
BlastJob	biomobyobject	A BLAST job.
Password	biomobyobject	A generic password object.
Poll_Job	workflow
FASTA	biomobyobject	FASTA formatted sequence

Beanshells (3)

Name	Description	Inputs	Outputs
isRunning		status	isRunning
Correct_Moby_Object		inputXML	outputXML
DownloadURLWithBasicAuth	This Beanshell downloads a file to disk. The standard download local Java widgets don't handle URLs with HTTP(S) Basic Authentication, but this Beanshell can. When a webserver uses BasicAuth, a login and password can be coded as part of the URL using the following syntax: http(s)://login:password@www.some.website/my/great/tool/result.xml. This beanshel extracts the login and password from the URL and supplies them automatically to the webserver. This prevents Taverna from showing popup dialogs requesting the login and password from the user as this will be problematic for large workflows. Please note that the path where the downloaded file will be stored must be an absolute path to a folder ended with a slash. (Slash backward on Windows or a slash forward on Linux/Unix/Mac OS X.) The filename for the result is automatically extracted from the URL.	theURL	blastResults

Outputs (1)

Name	Description
BlatResults

Links (15)

Source	Sink
BlastJob:mobyData	MobyBlast_submit:BlastJob(input)
DataBase:mobyData	BlastJob:DataBase(database)
DataBaseName	DataBase:id
Email:mobyData	User:Email(email)
FASTA:mobyData	BlastJob:FASTA(fasta)
MobyBlast_submit:BlastJob(output)	Poll_Job:BlastJob
MobyBlast_submit:URL(result)	Parse_Moby_Data_URL:mobyData('URL')
Parse_Moby_Data_URL:id	Flatten_urls:stringlist
Password:mobyData	User:Password(password)
Program:mobyData	BlastJob:Program(program)
Sequences	String:value
DownloadURLWithBasicAuth:blastResults	BlatResults
Flatten_urls:concatenated	DownloadURLWithBasicAuth:theURL
String:mobyData	FASTA:String(content)
User:mobyData	MobyBlast_submit:User(user)