UGENE Forum - introducting perl script into ugene as element in workflow

Apr 25^th, 2011 at 4:24pm

Poh Offline
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Hi!

I have a bunch of script formation a file format to the other in perl.

I am interested to know how can I introduce the script into ugene as a ugene element in the workflow designer?

Is there a way to put in plugins in ugene?

Thanks.

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Reply #1 - Apr 25^th, 2011 at 6:04pm

Mikhail Fursov Offline
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Hi!
To add scripting support for your favorite language in UGENE's Workflow Designer you need the following

1) Think about data model mapping: all algorithms in UGENE use common data model. So your script must output in some form (either file or stdout) data that your adapter in UGENE will be able to parse and create UGENE data models

2) Check "Create Script Object" toolbar action. It allows you creating custom script objects using QtScript (JavaScript).
Clone it to serve your needs.

Hope it helps.

---
UGENE team

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Reply #2 - Apr 27^th, 2011 at 3:40pm

Poh Offline
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Posts: 46

Is there a simple hello world example on it?

I am looking at just try out a few script with a define input file and run it, output text file and that's it.

I am not sure of the common data model. Still looking.

Thanks.

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Reply #3 - Apr 28^th, 2011 at 4:25pm

Poh Offline
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Posts: 46

I manage to do a read and write file. It looks working, but not yet with scripting....

Any pointers if I am to add a component in between read write to convert character from xxx to yyy or something like that?

Thanks.

ugeneReadWrite.JPG (170 KB | )

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Reply #4 - Apr 28^th, 2011 at 5:26pm

Poh Offline
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Posts: 46

ok I tried. but cannot find where can I put in the code in parameter to call the perl scripts..

Any pointers?

ugenescripting.JPG (162 KB | )

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Reply #5 - Apr 28^th, 2011 at 6:20pm

Mikhail Fursov Offline
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Poh wrote on Apr 27^th, 2011 at 3:40pm:

Is there a simple hello world example on it?

I am looking at just try out a few script with a define input file and run it, output text file and that's it.

I am not sure of the common data model. Still looking.

Thanks.

There is no simple or standard way to integrate script engine into the application. The example with QT script actually uses QScriptEngine from QT that is different from running an independent standalone app.
May be we should think and introduce a framework here to simplify use other languages with UGENE: https://ugene.unipro.ru/tracker/browse/UGENE-253

Common data model is very simple. Start with DNASequence. To use it in the simplest way the only you need is a) name b) sequence c) alphabet
You need to create a wrapper for your script to parse it results and create DNASequence object.

---
UGENE team

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Reply #6 - Apr 29^th, 2011 at 8:59am

Poh Offline
YaBB Newbies

Posts: 46

ok.

Sequencing files are one of the common start point for sequence analysis.

However, many highthroughput data are not sequence based. For example, genotyping data from microarray.

It exist in the form like this.
organism genotype1 genotype2 genotype3
ABC    11 00 10
BCA    10 11 10

Then the data are needed to be converted to (usually done with the script)

INPUT ABC BCA
G1    AA AB
G2    BB AA
G3    AB AB

Enabling a much more generic interface to enable end users to create element to process data, empowering end user to wrap in scripts they found/write and put it as element into ugene would be a very powerful feature. Plus the ability to run it local and grid would be well leveraged.

Besides that helps makes ugene a much more flexible tool if users started to share their pipeline via uwl. That can help alot in the prototyping effort before a much more polished pipeline integrated to the mainstream of ugene capabilities. Enabling that too will lighten the load of ugene developers as users around the world shares.

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