Problems installing the new VCF File Visualization tool VIVA

Question

[gcooper1245]

I have been following the guide the recently published Nature paper linked on Github. I have been able to install Julia and add it to my path. Yet, when I try to run the block of code they suggest in the the next step to install the package, it returns this error

-bash: syntax error near unexpected token `('

I am using a MacOSX version 10.14.5. Has anyone else been able to install this program successfully? Any help would be appreciated.

[Alewa]

sorry which specific line of the codes were you referring to?

julia
]add VariantVisualization
exit()

https://github.com/compbiocore/VariantVisualization.jl

[Alewa]

Ok! I assume you have cloned the github Repo if you haven't done it yet, you can follow the tutorial on github page; https://help.github.com/en/github/creating-cloning-and-archiving-repositories/cloning-a-repository

try this instead on the command line $ julia VariantVisualization.jl while making sure that the VariantVisualization.jl is in the current working directory or point to the exact location of VariantVisualization.jl on your local computer.

[gcooper1245]

Yes I am talking about Step 2. So I cloned the VariantVisualizaton.jl into my local, and when I tried to run the same command you pasted above, it returned this.

julia
]add VariantVisualization
exit()               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.2.0 (2019-08-20)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

(v1.2) pkg> add VariantVisualization
  Updating registry at `~/.julia/registries/General`
  Updating git-repo `https://github.com/JuliaRegistries/General.git`
 Resolving package versions...
  Updating `~/.julia/environments/v1.2/Project.toml`
 [no changes]
  Updating `~/.julia/environments/v1.2/Manifest.toml`
 [no changes]

(v1.2) pkg> exit()

Then when I follow the next step and open up a new terminal, the viva command cannot be found. It appears that it is not installing the right tool.

[gcooper1245]

And if I try what you said, it returns this.

  julia VariantVisualization.jl/
ERROR: could not open file /Users/garrettcooper/Documents/Bioinformatics/VariantVisualization/VariantVisualization.jl/
Stacktrace:
 [1] include at ./boot.jl:328 [inlined]
 [2] include_relative(::Module, ::String) at ./loading.jl:1094
 [3] include(::Module, ::String) at ./Base.jl:31
 [4] exec_options(::Base.JLOptions) at ./client.jl:295
 [5] _start() at ./client.jl:464

[Mark]

Which code exactly? Is it step 2?

edit: IMO that's a horrible installation setup. Not really worth it for.. what 2 heat maps it produces?

[gcooper1245]

Do you have another tool you think would be easier to visualize VCF's?

[Mark]

For me vcfR + your fav visualisation tool will happily do. The manual of vcfR is really good and demonstrates several possible visualisations possible: https://knausb.github.io/vcfR_documentation/index.html