plugin SmallRNAPlugin not found.

[athanasy-ljw]

Dear JBrowse development group,

I downloaded the SmallRNAPlugin and set jbrowse. conf, but JBrowse reported that the SmallRNAPlugin could not be found.I don't know how to solve this problem.Could you please guide me on this?

I thank you for your time. Cheers, Jiawei_Li

[jefftung]

Hi Jiawei, Looking at the third image, the other plugins (bookmarks, NeatCanvasFeatures, etc) all have a location of "../plugin/.." while the smallRNAPlugin only have "plugins/SmallRNAPlugin". It could be the location of the plugin is incorrect. Make sure the location is correct; perhaps you should try "../plugins/SmallRNAPlugin" as the location. I would delete the lines you added in the .json file.

Hope this help! Jeff

[athanasy-ljw]

Hi Jeff，

Thank you very much for your reply. I changed the path to "../ plugins /.." It still doesn't work. And then I wrote the absolute path, but it still couldn't find the plugin. I found that the path of the other plugins (bookmarks, NeatCanvasFeatures, etc) seemed to be wrong, The JBrowse folder contains the plugins folder, not the plugin folder.

Cheers, Jiawei_Li

[jefftung]

Hi Jiawei,

question: If you delete the lines you added to the jbrowse_conf.json file, and add "#" to the two lines in jbrowse.conf file, does jbrowse work?

[athanasy-ljw]

Hi Jeff，

I changed the file contents as you said, and JBrowse can work normally.

[jefftung]

Good! I want to see the "bookmarks" plugin working. So, can you take a screenshot of the jbrowse when you click on tools?

[athanasy-ljw]

The "bookmarks" plugin appears to work.

[jefftung]

Good! A couple of questions:

1. Is there a folder for the "bookmarks" plugin in the "plugins" folder?
2. did you run "./setup.sh" again after you download the "smallrnaplugin"?

[athanasy-ljw]

1. There is a "bookmarks" plugin folder in the "plugins" folder.

2. I run "./setup.sh" again when I downloaded the "smallrnaplugin" ,but run failed,I don't know why..

[jefftung]

so that's the problem. when you run "./setup.sh" after downloading the plugin, it needs to complete without failing.

1. do you have more than one folder of "jbrowse"?
2. what happens if you change the location of the "bookmarks" plugin to : ../plugins/bookmarks
3. what is the error message when you re-run "./setup.sh"?

[athanasy-ljw]

1. Yes, I have more than one folder of "jbrowse".
2. I change the location of the "bookmarks" plugin to : ../plugins/bookmarks, JBrowse works
3. I deleted the error message earlier... But I can run "./setup.sh" again,which may take some time. I'll send you the error message when it's finished. Thanks

[athanasy-ljw]

[jefftung]

1. which jbrowse folder is the screenshot of the jbrowse that is currently working from? i think your url should be something like "xxxxx/yyyy". The "yyyy" should match the name of the folder of your jbrowse.
2. are the jbrowse folder the same versions? your error message looks like the one I had before(I don't remember the exact message but it looks the same). I just download 2 different versions of jbrowse developer version and re-run "./setup.sh" with the plugins download. That solved my problem with the "./setup.sh" error.

[athanasy-ljw]

1. Yes, I know this, the name of the JBrowse folder and my url match each other.

2. Yes, all the JBrowse folders are the same version, because I made multiple copies and put them on different websites.

3. So now I need to re-download a new JBrowse(Do I need to delete all of the current JBrowse?) and then download the "smallrnaplugin" before running the "./setup.sh"?

[jefftung]

I'm not sure how you setup the multiple copies of JBrowse so I'm not sure if my method will solve your problem. I would keep all the JBrowse copies you have. Download a new developer's version of JBrowse that your system does not have. Download or copy (do not make shortcuts or alias or links) all the plugins you want to use to this new JBrowse folder. Run "./setup.sh". Good luck!