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vgteam / sequenceTubeMap

displays multiple genomic sequences in the form of a tube map
MIT License
177 stars 24 forks source link

vg chunk failed #411

Open this-is-Mayank opened 5 months ago

this-is-Mayank commented 5 months ago

Screenshot 2024-03-21 204847

I tried building and running vgteam on my computer locally but I could not see any of the preinstalled visualizations. As you can see in the attached screenshot, it says 'vg chunk failed:'. What are possible fixes for this? Thank you!

gforg34 commented 3 months ago

Hi @this-is-Mayank ,

I am dealing with the same error. I found out a solved thread #176 which apparently solves the problems using thread #178. However, I do not understand at all how they fix it and how can I do it. It seems rather complicated to me. I don't know if you've figured out this problem yet.

Thanks.

its-me-Mayank commented 3 months ago

Hello @gforg34 ,

Yes, I figured it out. My problem was that vg was not being installed correctly. I had to manually install a few dependencies.

Hope this helps. Let me know if you want to try this fix.

Mayank.

gforg34 commented 3 months ago

Hi @its-me-Mayank ,

Thanks for your immediate reply. I don't know if it is possible for you and share your steps regarding this issue. I notice that I have a dependency problem downloading vg, which is also a software created by the same team like sequenceTube. How did you manage to solve this? Do you recall?

its-me-Mayank commented 2 months ago

Hi @gforg34 ,

I am trying to install sequenceTubeMapping on a new virtual machine. I am thinking of documenting the process and taking a note of what exactly has to be changed from the guide in the readme page of the repository. The problem, I think, is being caused because of outdated versions of certain dependencies of vg.

I will let you know when I have something. Good Day.

gforg34 commented 2 months ago

Hi @its-me-Mayank ,

Thank you for help on this. So I also figured out the problem with the vg dependencies by install it using conda. In general, I had many issues downloading vg, but conda did it for me. Then I run SequenceTubeMap in the conda environment and it works perfectly. However, thanks for your willingness to help and your time.