Sff2Fasta_Blast_ParseBlast

Created: 2010-09-22 12:40:55 Last updated: 2010-09-22 13:35:26

Download Workflow

Blast Roche 454 sequences against a reference database on the Dutch Life Science Grid

Conversion of Roche 454 sequences to fasta
Blast sequences against a database
Parse Blast results

http://www.bioinformaticslaboratory.nl/

Preview

Download as scalable diagram (SVG)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/1525/download?version=1
[ More Info Expand ]

Workflow Components

Inputs (3)

Name	Description
SffFile
DatabaseFastaGz
MaxBlastHitsPerEntry

Processors (6)

Name	Type	Description
config_Blast	stringconstant
config_Sff2Fasta	stringconstant
Blast	arbitrarywsdl	Service definition of function ns__GASWexecution
config_ParseBlast	stringconstant
ParseBlast	arbitrarywsdl	Service definition of function ns__GASWexecution
Sff2Fasta	arbitrarywsdl	Service definition of function ns__GASWexecution

Beanshells (0)

Outputs (5)

Name	Description
FastaFile
QualFile
FlowFile
BlastOutTarGz
ParsedBlastTxt

Links (13)

Source	Sink
DatabaseFastaGz	Blast:input1
MaxBlastHitsPerEntry	ParseBlast:input0
SffFile	Sff2Fasta:input0
Blast:result0	BlastOutTarGz
Blast:result0	ParseBlast:input1
Sff2Fasta:result0	Blast:input0
ParseBlast:result0	ParsedBlastTxt
Sff2Fasta:result0	FastaFile
Sff2Fasta:result1	QualFile
Sff2Fasta:result2	FlowFile
config_Blast:value	Blast:config-file
config_ParseBlast:value	ParseBlast:config-file
config_Sff2Fasta:value	Sff2Fasta:config-file

Coordinations (0)

Information Workflow Type

Taverna 1

Information Uploader

Barbera van Schaik

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (4)

(People/Groups)

Information Attributions (0)

(Workflows/Files)

None

Information Tags (9)

Uploader tags

alignment
|
BLAST
|
conversion
|
DNA
|
grid
|
moteur
|
sequence
|
taverna
|
vbrowser

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

2050 viewings

1718 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

Sff2Fasta_Blast_ParseBlast

Created by Barbera van Schaik on Wednesday 22 September 2010 12:40:55 (UTC)

Last edited by Barbera van Schaik on Wednesday 22 September 2010 13:35:26 (UTC)

Reviews (0)

No reviews yet

Be the first to review!

Comments (0)

View Timeline

No comments yet

Log in to make a comment

Other workflows that use similar services (7)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.

Taverna 1

Uploader

Glatard

feat (3)

This is an attempt to implement the feat application from the fsl fMRI package www.fmrib.ox.ac.uk/fsl/fsl/whatsnew.html into a Scufl workflow. Details are still being polished but the general structure is here. The main problem that we have with such workflows concerns data provenance. Each of the services is typically iterated on hundreds of data sets and keeping track of the produced files is a pain.

Created: 2008-03-18 | Last updated: 2008-05-19

Credits: Glatard

Taverna 1

Uploader

Glatard

Sample grid workflow (1)

Download

This is a sample workflow submitting jobs to the EGEE grid using the Generic Application Service Wrapper (GASW). The job submission service has to be installed locally.

Created: 2008-10-24 | Last updated: 2008-10-31

Credits: Glatard