DNA sequence analysis pilot (Blat)

Created: 2009-11-20 11:12:43 Last updated: 2009-11-30 09:35:38

Download Workflow

http://amc-app1.amc.sara.nl/twiki4/bin/view/BioLab

Workflow-based DNA sequence analysis on the Dutch Life Science Grid.

This workflow is based on http://www.myexperiment.org/workflows/840 , the last component (Blast analysis) is replaced by Blat analysis

Preview

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://myexperiment.org/workflows/960/download?version=1
[ More Info Expand ]

Workflow Components

Inputs (3)

Name	Description
sffTar
patternFile
referenceTar

Processors (9)

Name	Type	Description
BlatConfigFile	stringconstant
sff2fasta_configfile	stringconstant
empty	stringconstant
patternMatch_configfile	stringconstant
patternMatch	arbitrarywsdl	Service definition of function ns__GASWexecution
sffToFasta	arbitrarywsdl	Service definition of function ns__GASWexecution
Blat	arbitrarywsdl	Service definition of function ns__GASWexecution
sffExecutable	stringconstant
blatExe	stringconstant

Beanshells (0)

Outputs (3)

Name	Description
BlatTarFile
qualOutputTarFile
txtOutputTarFile

Links (15)

Source	Sink
patternFile	patternMatch:input2
empty:value	sffToFasta:command-line
sff2fasta_configfile:value	sffToFasta:config-file
sffTar	sffToFasta:input0
BlatConfigFile:value	Blat:config-file
patternMatch:result0	Blat:input0
patternMatch_configfile:value	patternMatch:config-file
referenceTar	Blat:input2
blatExe:value	Blat:input1
sffExecutable:value	sffToFasta:input1
patternMatch:result1	qualOutputTarFile
patternMatch:result2	txtOutputTarFile
sffToFasta:result0	patternMatch:input0
sffToFasta:result1	patternMatch:input1
Blat:result0	BlatTarFile

Coordinations (0)

Information Workflow Type

Taverna 1

Information Uploader

Angela Luijf

Information License

All versions of this Workflow are licensed under:

Information Version 1 (earliest) (of 2)

Information Credits (3)

(People/Groups)

Information Attributions (1)

(Workflows/Files)

DNA sequence analysis pilot

Information Tags (7)

Uploader tags

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

3654 viewings

2129 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

DNA sequence analysis pilot (Blat)

Created by Angela Luijf on Friday 20 November 2009 10:50:13 (UTC)

Last edited by Angela Luijf on Friday 20 November 2009 11:06:56 (UTC)
DNA sequence analysis pilot (Blat)

Created by Angela Luijf on Friday 20 November 2009 11:12:43 (UTC)

Last edited by Angela Luijf on Monday 30 November 2009 09:35:39 (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