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neherlab / pan-genome-visualization

Visualization of the pan-genome output by panX
https://pangenome.ch
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localhost:800/my_species loads, I can view the Gene Cluster but no "Sequence Alignment" and no "Gene Tree" #7

Open NA1919 opened 3 years ago

NA1919 commented 3 years ago

Hello,

I had panX some weeks ago and it was working perfectly, but I had to run tun the analysis again to add some new sequences. So with my new, larger dataset it does not work anymore. When I try to view my own data (as described with npm and localhost:800/), I see the Gene Cluster Table and the Strain Tree, But it does not let me chose and change anything. the sections "Sequence Alignment" and "Gene Tree" are always empty. When I view the TestSet, I can click on the items of the Gene Cluster Table but even if I click (and the line is marked/chosen), I cannot see any sequences. npm starts without any errors, although with this warning that I don't understand "WARNING in webpack: Using NoErrorsPlugin is deprecated. Use NoEmitOnErrorsPlugin instead." I don't see any other errors. When I try to view the old dataset -the one that had worked some weeks ago- I'm having the same issues.

Is there a way for me to figure out what might cause this problem? As far as I can tell, the analysis ran smoothly and the output seems fine.

Thank you in advance for any help :) Nurper

hyoj-seo commented 3 years ago

Hello,

I had the same problem as you. There seems to be no problem with my files.

Have you ever solved this problem? I can't find an answer to this question, so I'm inevitably leaving a reply.

thank you for your help. hj

NA1919 commented 3 years ago

Hey, no this never worked out for me :( unfortunately I still have no idea why Good luck to you! :)

Isoris commented 1 year ago

Same here guys. It's really annoying that everytime a nice tools is created, it is so poorly explained and not even maintained.. such a pity

ivan-aksamentov commented 1 year ago

Hi Quentin @Isoris

I have written a little guide on how to run the tool currently:

https://github.com/neherlab/pan-genome-visualization/blob/master/README.md

There is also a neighbor branch where we discuss roughly the same:

https://github.com/neherlab/pan-genome-visualization/issues/16

Feel free to give it a try and let me know how it goes!

Isoris commented 1 year ago

Hello Ivan! Thank you so much for the information, I really appreciate your commitment. I will give it a look tomorrow morning. 😁 That's awesome! ~

Quentin.