BlatBlastCombi

Created: 2009-02-03 08:20:43 Last updated: 2009-02-03 08:28:06

Download Workflow

This workflow combines the blat and blast workflows. It takes as input a database name (Danio_rerio_Genome for Zebra Fish for example) and and a set of Fasta sequences. It first tries to perform a blat (at www.bioinformatics.nl). When this service returns nothing, a blast is done (also at www.bioinformatics.nl). The resulting reports are combined.

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

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://myexperiment.org/workflows/531/download?version=1
[ More Info Expand ]

Workflow Components

Inputs (2)

Name	Description
DataBaseName
Sequences

Processors (10)

Name	Type	Description
Create_Sequence_Chunks	beanshell
Flatten_list	local
Split_sequences	beanshell
Merge_string_list_to_string	local
Chunk_Size	stringconstant
Merge_string_list_to_string1	local
Write_Text_File	local
Write_Text_File1	local
DoBioMart	workflow
BlatOrBlast	workflow

Beanshells (10)

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
Download_Report_and_Filter	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.	URL eValue	blatResults
EmptyList			list
Join_Blat_Blast_Results		list1 list2	outputList
isEmpty		string	isEmpty
Filter_Sequences_For_Blast		sequences blatResult	sequencesForBlast
Create_Sequence_Chunks		sequences chunkSize	chunks
Split_sequences		sequenceText	sequences

Outputs (2)

Name	Description
Alignments
BioMartRecord

Links (13)

Source	Sink
DataBaseName	BlatOrBlast:DataBaseName
Sequences	Split_sequences:sequenceText
BlatOrBlast:Alignments	Flatten_list:inputlist
Chunk_Size:value	Create_Sequence_Chunks:chunkSize
Create_Sequence_Chunks:chunks	BlatOrBlast:Sequences
DoBioMart:records	Merge_string_list_to_string1:stringlist
DoBioMart:records	BioMartRecord
Flatten_list:outputlist	Alignments
Flatten_list:outputlist	DoBioMart:blastRecord
Flatten_list:outputlist	Merge_string_list_to_string:stringlist
Merge_string_list_to_string1:concatenated	Write_Text_File1:filecontents
Merge_string_list_to_string:concatenated	Write_Text_File:filecontents
Split_sequences:sequences	Create_Sequence_Chunks:sequences