Greetings, I am looking for information, tips, and pointers on writing a component for visualizing text data in Galaxy. In particular I would like to use Brat (http://brat.nlplab.org/embed.html) which can be embedded in web pages/apps. The “Implementation Details” section on the Learn/Visualization page (https://wiki.galaxyproject.org/Learn/Visualization#Implementation_Details) hints at exactly what I want to do: - use AJAX to fetch JSON data. - use a Javascript client to draw the data I can do both of the above steps, I am just not sure how to wire Brat into Galaxy. All of the documentation I can find about visualization covers installing existing Genome visualization tools and nothing about how to adapt an existing Javascript client to work in Galaxy. I am hoping someone can sketch out the basic steps I need to accomplish before I spend too much time grepping through the Galaxy code base. Cheers, Keith ------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
Hi Keith, I'm a fan of learning by eyample, so please find attached the BRAT VIS :) Put the folder into your ./config/plugins/visualizations/ folder and restart Galaxy. You should see a new visualisation in every text datatype in your Galaxy history. (We should change this later to JSON). Have a look at the nlp_brat.xml file in config and the nlp_brat.mako file. This is everything what you need to adopt or change if you want to create a VIS. Hope this helps, Bjoern
Greetings,
I am looking for information, tips, and pointers on writing a component for visualizing text data in Galaxy. In particular I would like to use Brat (http://brat.nlplab.org/embed.html) which can be embedded in web pages/apps. The “Implementation Details” section on the Learn/Visualization page (https://wiki.galaxyproject.org/Learn/Visualization#Implementation_Details) hints at exactly what I want to do: - use AJAX to fetch JSON data. - use a Javascript client to draw the data
I can do both of the above steps, I am just not sure how to wire Brat into Galaxy. All of the documentation I can find about visualization covers installing existing Genome visualization tools and nothing about how to adapt an existing Javascript client to work in Galaxy. I am hoping someone can sketch out the basic steps I need to accomplish before I spend too much time grepping through the Galaxy code base.
Cheers, Keith
------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
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Hi Keith, I'm a fan of learning by eyample, so please find attached the BRAT VIS :) Put the folder into your ./config/plugins/visualizations/ folder and restart Galaxy. You should see a new visualisation in every text datatype in your Galaxy history. (We should change this later to JSON). Have a look at the nlp_brat.xml file in config and the nlp_brat.mako file. This is everything what you need to adopt or change if you want to create a VIS. Hope this helps, Bjoern Am 24.05.2015 um 02:45 schrieb Keith Suderman:
Greetings,
I am looking for information, tips, and pointers on writing a component for visualizing text data in Galaxy. In particular I would like to use Brat (http://brat.nlplab.org/embed.html) which can be embedded in web pages/apps. The “Implementation Details” section on the Learn/Visualization page (https://wiki.galaxyproject.org/Learn/Visualization#Implementation_Details) hints at exactly what I want to do: - use AJAX to fetch JSON data. - use a Javascript client to draw the data
I can do both of the above steps, I am just not sure how to wire Brat into Galaxy. All of the documentation I can find about visualization covers installing existing Genome visualization tools and nothing about how to adapt an existing Javascript client to work in Galaxy. I am hoping someone can sketch out the basic steps I need to accomplish before I spend too much time grepping through the Galaxy code base.
Cheers, Keith
------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Björn, Brilliant! Thanks. That is exactly what I was looking for. Cheers, Keith On May 24, 2015, at 4:49 AM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Keith,
I'm a fan of learning by eyample, so please find attached the BRAT VIS :)
Put the folder into your ./config/plugins/visualizations/ folder and restart Galaxy. You should see a new visualisation in every text datatype in your Galaxy history. (We should change this later to JSON).
Have a look at the nlp_brat.xml file in config and the nlp_brat.mako file. This is everything what you need to adopt or change if you want to create a VIS.
Hope this helps, Bjoern
Am 24.05.2015 um 02:45 schrieb Keith Suderman:
Greetings,
I am looking for information, tips, and pointers on writing a component for visualizing text data in Galaxy. In particular I would like to use Brat (http://brat.nlplab.org/embed.html) which can be embedded in web pages/apps. The “Implementation Details” section on the Learn/Visualization page (https://wiki.galaxyproject.org/Learn/Visualization#Implementation_Details) hints at exactly what I want to do: - use AJAX to fetch JSON data. - use a Javascript client to draw the data
I can do both of the above steps, I am just not sure how to wire Brat into Galaxy. All of the documentation I can find about visualization covers installing existing Genome visualization tools and nothing about how to adapt an existing Javascript client to work in Galaxy. I am hoping someone can sketch out the basic steps I need to accomplish before I spend too much time grepping through the Galaxy code base.
Cheers, Keith
------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
<nlp_brat.tar.bz2>
------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
participants (2)
-
Björn Grüning -
Keith Suderman