Question: Installation of a Visualization in my local instance of galaxy
1
gravatar for rlee03
2.3 years ago by
rlee0350
United States
rlee0350 wrote:

Hi! 

I am trying to load a crossbio visualization onto my local instance of galaxy. 

Per the "The Visualizations Registry" wiki in Galaxy,  

1) I configured the  galaxy.ini file   by uncommenting  "visualizations_plugins_directory = config/plugins/visualizations" 

2) I copied and pasted the folder crossbio visualization into the appropriate folder  (config/plugins/visualizations)

     crossbio/config/crossbio_blast.xml

     crossbio/static/css/bootstrap.css

     crossbio/static/css/dc.ss

     crossbio/static/js/biojsioblast.js

    crossbio/static/js/crossbio.js

     crossbio/templates/crossbio_blast.mako

Unfortunately, my server log is not even recognizing this visualization as a loaded plugin. Any help would be very much appreciated. Thanks.

   

visualization local galaxy xml • 921 views
ADD COMMENTlink modified 2.2 years ago • written 2.3 years ago by rlee0350

Hi carl, 

see googledrive https://drive.google.com/open?id=0B-J0sIwOpVwAb21ySi1SajhDbVU  . Thanks!

-Roy

ADD REPLYlink written 2.2 years ago by rlee0350
1

Hi, Roy

It looks like your crossbio_blast.xml is the github html page for that file instead of the actual file. It may be that it was accidentally downloaded. I'd recommend:

  1. Deleting your existing crossbio directory 'config/plugins/visualizations/crossbio'
  2. using git clone to clone https://github.com/bgruening/galaxy_blast/tree/b324ba9efa9e9d579445bf4fd352d2b0c39990fd (the entire repo) either to the above directory or where-ever you like (you can remove it after you copy the visualizations sub-directory). Further info here: https://help.github.com/articles/cloning-a-repository/
  3. moving only the subdirectory: mv galaxy_blast/visualizations/crossbio_blast  config/plugins/visualizations/
  4. re-starting the server

 

ADD REPLYlink written 2.2 years ago by carlfeberhard390

these are excellent directions. Thank you. Also would you happen to know where on the galaxy GUI this shows up? e.g. how would I upload the blast xml output as the input for crossbio?

Thank you.

ADD REPLYlink written 2.2 years ago by rlee0350
1

In the history panel on the right of your main page, expand a blast dataset and you'll be able to see a button that looks like a bar graph. Click that button (where the arrow points below) and a submenu should appear that contains a link to the crossbio visualization.

Visualization button in the history

ADD REPLYlink written 2.2 years ago by carlfeberhard390

Hi Carl, Sorry to keep bugging you with a bunch of questions. Thanks. I went through a series of uploads w/ various blast upload datatypes and cannot view this icon in the history. Could it be possible that I must adjust the galaxy ini file?

Below are my screen shots, I'm working out of docker images if that helps. Thank you.

https://drive.google.com/open?id=0B-J0sIwOpVwAMnFWOXBub2NCQm8

ADD REPLYlink written 2.2 years ago by rlee0350

The visualization icon does show up for interval files, but the drop down option for crossbio Js doesn't exist. Only visualizations of scatterplot & trackster exist as options in history dropdown menu.

ADD REPLYlink written 2.2 years ago by rlee0350

Hi, Roy

It looks like the plugin is loading fine based on the third and fourth screenshots. I think what's happening here is that the datatype needed by the plugin (https://github.com/bgruening/galaxy_blast/blob/b324ba9efa9e9d579445bf4fd352d2b0c39990fd/visualizations/crossbio_blast/config/crossbio_blast.xml#L7) 'blastXML' isn't matching the datatype of your dataset ('xml' according to the firt screenshot. These two must match for the visualization to be considered 'applicable' to the dataset and shown in the dropdown.

So, I'd recommend changing the datatype. If you edit the attributes of your dataset (using the button with the pencil icon), go to the datatype tab in the center pane, and then use the dropdown to search for blastxml, does it appear? If so, select that datatype and click save. Galaxy will work on the metadata for a moment - then, try again to find crossbio_blast in the visualization dropdown in the dataset.

ADD REPLYlink written 2.2 years ago by carlfeberhard390

Thank you very much for your guidance up until this point.

1) when I upload a sample Blast.xml output file as my test data , the Visualizer does NOT appear on the right side of the galaxy GUI (slide 1) . 1a) inside the crossbio_blast.xml ....."datatype">blast.BlastXml</test> , is blast is the file extension of the upload inherited from BlastXml? I asked question 1a, because 1b) when I switched "datatype">blast.BlastXml</test> to "datatype">xml.GenericXml</test> AND again uploaded the Blast.xml file test data, the Visualizer does DOES appear on the right side of the galaxy GUI. Can you confirm that the xml is the extension inherited from the GenericXml ? (slide 2) The Blast visualizer only returns a blank result. (also see slide 2, middle section).

2) My potential plan, 2a) would I need to alter the /home/galaxy/config/datatypes_conf.xml.sample to add the blast data type? since you I was initially given the following datatypes datatype">blast.BlastXml</test>? e.g.

ADD REPLYlink written 2.2 years ago by rlee0350

I'm also having the same problem as rlee03. I've added the crossbio_blast directory from the git repository and copied it into config/plugins/visualizations and restarted galaxy following the instructions in this thread. I see no errors relating to crossbio in the paster.log file. However, I cannot use crossbio_blast with a blastxml output file. Does anyone have any suggestions?

 

ADD REPLYlink written 2.2 years ago by danielfortin86100

Hi, Roy and Daniel

(This is in response to Roy's comment dated Oct. 8th and Daniel's first comment)

I've tested the visualization in Björn's repo and made some changes. Please see the updated repository here:

https://github.com/bgruening/galaxy_blast/tree/blast_xml_vis

  1. Update your visualizations to the crossbio_blast visualization in that repo,
  2. make sure you have the blast datatypes installed into your instance (e.g. BlastXml.BlastXml)
  3. restart your server
  4. upload (or run a tool that produces) a blastxml dataset
  5. find and click the visualization as shown in my screenshot of the dataset visualization menu: https://biostar.galaxyproject.org/p/14022/#14350
  6. let me know if that does not work
ADD REPLYlink written 2.2 years ago by carlfeberhard390

Hi Carl,

The changes you made to indeed allow me to see the "Visualize" and "BLAST XML Viewer"  option. However, when I click it the visualization does not appear. The only thing I see is the following text:

selected out of records
Sequence identitiy
Length distribution
Score distribution
Organisms
Proteins
HSSP

I've tried this with several sequence queries and I get the same results

Thanks

ADD REPLYlink written 2.2 years ago by danielfortin86100

Hi, Daniel

Can you open the javascript console and see if there are any errors there, please?

http://webmasters.stackexchange.com/questions/8525/how-to-open-the-javascript-console-in-different-browsers

ADD REPLYlink written 2.2 years ago by carlfeberhard390

Hi Carl,

It seems I'm missing the following:

http://localhost:8080/plugins/visualizations/crossbio_blast/static/js/dc.js.map

http://localhost:8080/plugins/visualizations/crossbio_blast/static/css/bootstrap.css.map

I presume this means I need to install bootstrap and dc.js?

ADD REPLYlink written 2.2 years ago by danielfortin86100

No - those are source maps and are not required to view the visualization.

That's all you see and there are no other errors? Are you in the console tab? What is the raw output of that tab when you load the visualization?

ADD REPLYlink written 2.2 years ago by carlfeberhard390

Sorry, there is one other line:

Uncaught TypeError: Cannot read property '1' of null 

crossbio_blast:135

Thanks!

ADD REPLYlink written 2.2 years ago by danielfortin86100

Hi Daniel,

I have a potential fix here: https://github.com/greenify/crossbio/pull/3

If this gets accepted I will update the vis accordingly.

Sorry for the trouble,

Bjoern

ADD REPLYlink written 2.2 years ago by Bjoern Gruening4.8k

Alright. re: TypeError: that makes more sense and I've seen that before. I believe it has to do with the file parsing here:

https://github.com/bgruening/galaxy_blast/blob/blast_xml_vis/visualizations/crossbio_blast/templates/crossbio_blast.mako#L137

I'll ping Bjorn about that. In the meantime, would you mind uploading this test file and see if that allows the visualization:

https://raw.githubusercontent.com/bgruening/galaxy_blast/blast_xml_vis/test-data/blastp_sample.xml

ADD REPLYlink written 2.2 years ago by carlfeberhard390

Hi Carl,

The example you linked to does work in my local instance! Let me know if / when changes are made to make this functional 

Thanks!

ADD REPLYlink written 2.2 years ago by danielfortin86100

this example also works on my local instance! Great! Thanks everyone. Same here, let me know when changes are made for this functionality.

ADD REPLYlink written 2.1 years ago by rlee0350
2
gravatar for carlfeberhard
2.2 years ago by
carlfeberhard390
United States
carlfeberhard390 wrote:

Hi, rlee03

Make sure you re-start the server. It does not automatically re-load the plugins when a folder is copied into that location. Also make sure your 'crossbio' directory is the same name as the basename of your config file:

# you have
crossbio/config/crossbio_blast.xml

# for it to be recognized as a plugin:
crossbio_blast/config/crossbio_blast.xml

If that doesn't work:

  • Can you post the server log message about your plugin (if any are printed).
  • Can you also post your config file ('crossbio_blast/config/crossbio_blast.xml')

(Edit:) I've updated the wiki to state 'The config file and mako file must share the same name as the plugin name / plugin directory':  https://wiki.galaxyproject.org/VisualizationsRegistry#Configuring_your_visualization_plugin_in_the_.60visualization_plugins_directory.60

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by carlfeberhard390

Hi,

I'm trying to implement crossbio on my local instance of galaxy, by copying these files w/ their respective locations in my local galaxy instance.

https://github.com/bgruening/galaxy_blast/tree/b324ba9efa9e9d579445bf4fd352d2b0c39990fd/visualizations/crossbio_blast

1) I placed them in the following folder:

/home/galaxy/config/plugins/visualizations/

The folder inside visualizations (called crossbio_blast) matches the xml file (crossbio_blast.xml)

Unfortunately, I am still getting this type our error (see attached) ***notice on line 3, crossbio visualization shows up in the error log.

2) Is there any alterations I need to make on the xml files or any part of galaxy to ensure this visualization works? I looked at the Visualization Registry https://wiki.galaxyproject.org/VisualizationsRegistry but still couldn't fix it.

3) This was the parsing error I got when opening up the XML in a webbrowser

(screenshots and XML files are all attached)

Your help would be very much appreciated. Thanks.

ADD REPLYlink written 2.2 years ago by rlee0350

Hi again, rlee03

There doesn't seem to be any screenshots or logs attached. Can you try attaching them again?

ADD REPLYlink written 2.2 years ago by carlfeberhard390
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