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Tutorials or documentation for UGENE plugin writing (Read 13638 times)

May 12^th, 2009 at 8:49am

Jonathan Wilson Offline
YaBB Newbies

Posts: 1

Is there any documentation on the UGENE APIs used when writing plug-ins?
Are there any tutorials out there for writing UGENE plug-ins?
Are there any examples of very simple plug-ins or are the only examples those in the UGENE code itself?

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Reply #1 - May 12^th, 2009 at 7:14pm

Ivan Efremov Offline
YaBB Administrator
Novosibirsk

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Posts: 46

Hello Jonathan, thank you for your interest in UGENE.

Quote:

Is there any documentation on the UGENE APIs used when writing plug-ins?
Are there any tutorials out there for writing UGENE plug-ins?

No, currently there is not.

Quote:

Are there any examples of very simple plug-ins or are the only examples those in the UGENE code itself?

There are some very simple and useful for educating plugins in UGENE source code, for instance perf_monitor and dna_export.

Do you have plans about contributing to UGENE?

UGENE team

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Reply #2 - Sep 20^th, 2011 at 7:16pm

Loddi Offline
YaBB Newbies

Posts: 5

Hi, is there any update on the plugin tutorial issue? I would like to contribute to UGENE by adding a plugin for RNA-SEQ Data visualization (SAM/BAM-viewer like). However some starting point would be needed to dig into the matter.

Thanks,
-Loddi

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Reply #3 - Sep 22^nd, 2011 at 9:09pm

Mikhail Fursov Offline
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Posts: 162

There are no developer oriented docs now. Reason: we have started migration to new type of data handling API that is not stable now, while old one has become obsolete.

Writing a simple plugin is very simple: just copy a small plugin like ORF marker into new directory and rename it. Plugin is a just a description plus entry function.

Once you have a plugin entry function called you need to run your own code. It can be a usual QT code or a plugin for existing view. ORF maker does inject some menues to the sequence view for example and you can check the code to do the same.

If you want to add SAM/BAM viewer like function, please check existing AssemblyBrowser: http://ugene.unipro.ru/images/ss_win7_assembly.png
If it matches your basic needs on visualization it's reasonable to extend/improve currect version functionality.

---
UGENE team

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Reply #4 - Sep 27^th, 2011 at 4:41am

Loddi Offline
YaBB Newbies

Posts: 5

Hey Mikhail,

thank you for the hints. Actually makeing an assemblyView display within an annotation/sequence view would be exactely what you need when analysing RNA-Seq data. However, currently it seems that these views can not be combined. One would also need to synchronize scrolling and zooming behavior of course. Another point would be the huge amount of reads usually sequenced through RNA-Seq Experiments. You would not need so much details on the reads as provided by the assembly viewer, actually a kind of coverage-graph would be sufficient in the beginning. Therefore I thought that it may be easier to use a simlified visualization like a custom graph data visualization as proposed before (http://ugene.unipro.ru/forum/YaBB.pl?num=1307557482/3#3) for other applications.

I'll take a look at the exsisting plugins and try to come up with an extension for the exisiting Graph-Plugin.

Regards,
-Loddi

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Reply #5 - Dec 20^th, 2019 at 3:25pm

kblag Offline
YaBB Newbies

Posts: 2

I think it's time to renew question

is there any documentation now in 2019 year?

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Reply #6 - Dec 20^th, 2019 at 3:58pm

Olga Golosova Offline
YaBB Administrator

Posts: 338

Quote:

I think it's time to renew question Smiley is there any documentation now in 2019 year?

What kind of plugin would you like to add?

If you've created a tool and would like to integrate it in UGENE and run with other tools in a workflow, try to use the feature, released in v. 33, see http://ugene.net/changelist.html. Further improvements of the feature are planned.

There still NO technical documentation for writing a plugin, however, we have commercial support services that may include the technical consultancy services.

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Reply #7 - Dec 20^th, 2019 at 5:50pm

kblag Offline
YaBB Newbies

Posts: 2

Quote:

What kind of plugin would you like to add?

nothing very complicated, but for example I want to add annotations from list of possible variants to the start and to the end of the primer sequence (like fluorophore and quencher in TaqMan) with one click. Or export sequences in format compatible with IDT (or any other) primers batch orders.

Currently I'm using Geneious and have plugings for such tasks. Maybe it can be done with Ugene workflows or tools integrations.

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Reply #8 - Dec 23^rd, 2019 at 5:28pm

Olga Golosova Offline
YaBB Administrator

Posts: 338

Quote:

export sequences in format compatible with IDT (or any other) primers batch orders.

Will FASTA format work for you? See e.g. "Sample fasta file" link here: https://eu.idtdna.com/calc/analyzer/home/batch.

To get the primers in FASTA format in UGENE, you can, for example, select the primer sequences in the Project View and export them into a new FASTA file, see https://ugene.net/wiki/display/UUOUM33/Exporting+Sequences+to+Sequence+Format.

Quote:

I want to add annotations from list of possible variants to the start and to the end of the primer sequence (like fluorophore and quencher in TaqMan) with one click.

Do you need some special visualization of fluorophores, etc.?
Could you please describe your scenario in more detail?
Possibly, using annotations for the primer sequences will work in this case.

In general, it seems you need to add some usability improvements to make your workspace handier. That's what we usually do in the commercial support services. So, you might consider to use them. Note that the changes we made are often included into the open-source UGENE version. And also UGENE training sessions are conducted to give you a jumpstart in using the software.

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