Workflow Entry: blastp of target vs source database

Created at: 19/03/10 @ 13:57:32 Last updated: 19/03/10 @ 14:05:40

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Version created on: 19/03/10 @ 13:57:32 by: Ian Laycock | Revision comments Expand

Last edited on: 19/03/10 @ 14:05:41 by: Ian Laycock

Title: blastp of target vs source database

Type: Taverna 2

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Description

This worlflow allows the user to input two sets of proteins in fasta format. One file is converted to a database using formatdb, the set is blasted against this database to test for Blast hits. Users is able to set eValue and destination of files for database and blast file. Arguments can be added to either formatdb or blast in beanshell supplied. Blast and formatdb must be installed locally and the correct filepaths for these applications must entered into the workflow accordingly.

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Workflow Components

Authors (3)

Titles (2)

Descriptions (2)

This workflow allows you to configure a BioMart query to fetch sequences you want from Ensembl. These sequences are retrieved and a blast database of them is created (by default, in the directory you ran taverna from). Warning: This workflow assumes that you have blastall and formatdb installed on the machine, and that by default, these are both found or linked in /usr/local/bin. It also assumes that you have write permission to the directory you have run taverna from. The beanshells "create_blastall_cmdArgs" and "create_formatdb_cmdArgs" are what you need to edit if the default locations are not appropriate for you. Shortcomings: The names of all the files created and used is hard coded in this workflow. This means that if you run this workflow more than once without editing anything, you will overwrite files you have previously created. All files created in the working directory are not yet coded to be deleted via the workflow. Ideally there would be an option that a user could choose that would set the files to be kept or deleted after use.

"This workflow allows you to configure a BioMart query to fetch sequences you want from Ensembl. These sequences are retrieved and a blast database of them is created (by default, in the directory you ran taverna from). Warning: This workflow assumes that you have blastall and formatdb installed on the machine, and that by default, these are both found or linked in /usr/local/bin. It also assumes that you have write permission to the directory you have run taverna from. The beanshells "create_blastall_cmdArgs" and "create_formatdb_cmdArgs" are what you need to edit if the default locations are not appropriate for you. Shortcomings: The names of all the files created and used is hard coded in this workflow. This means that if you run this workflow more than once without editing anything, you will overwrite files you have previously created. All files created in the working directory are not yet coded to be deleted via the workflow. Ideally there would be an option that a user could choose that would set the files to be kept or deleted after use."

Inputs (5)

Name	Description
targetProteins	Provide the name, and if not in your working directory, the location of the file of fasta sequence(s) that you wish to use to search the blast database created in this workflow.
sourceProteins	Filepath for source proteins Provide the name, and if not in your working directory, the location of the file of fasta sequence(s) that you wish to use to create the blast database in this workflow.
dbSave	name and filepath of created blast database
eValue	e value used for the blast
blastFile	filepath used to store the blast results in text format

Processors (7)

Name	Type	Description
create_blastall_cmdArgs	beanshell
create_formatdb_cmdArgs	beanshell
runBlastSearch	localworker
local_create_blastdb	localworker
runBlastSearch_command_defaultValue	stringconstant
local_create_blastdb_command_defaultValue	stringconstant
Read_Text_File	localworker

Beanshells (2)

Name	Description	Inputs	Outputs
create_blastall_cmdArgs		inputFilePath eValue dbSave outputFilePath	cmdArgsList
create_formatdb_cmdArgs		seqFile1 dbSave	cmdArgsList

Outputs (1)

Name	Description
Result	blast results of target against a source database in xml format

Datalinks (12)

Source	Sink
eValue	create_blastall_cmdArgs:eValue
dbSave	create_blastall_cmdArgs:dbSave
targetProteins	create_blastall_cmdArgs:inputFilePath
blastFile	create_blastall_cmdArgs:outputFilePath
sourceProteins	create_formatdb_cmdArgs:seqFile1
dbSave	create_formatdb_cmdArgs:dbSave
create_blastall_cmdArgs:cmdArgsList	runBlastSearch:args
runBlastSearch_command_defaultValue:value	runBlastSearch:command
create_formatdb_cmdArgs:cmdArgsList	local_create_blastdb:args
local_create_blastdb_command_defaultValue:value	local_create_blastdb:command
blastFile	Read_Text_File:fileurl
Read_Text_File:filecontents	Result