compiled binary files

[flystar233]

Can you provide compiled binary files? It's too difficult for Julia to install and use packages

[gtollefson]

@flystar233 Unfortunately, we are not currently able to offer compiled binary files containing an executable version of VIVA. However, we are working on this for a future release.

What part of the Julia language installation or package installation are you having trouble with? I would be happy to work with you to get Julia and our package installed so that you can use our VCF visualization tool, VIVA.

Join the Julia Slack community and send me a direct message. My Slack username is gtollefson. You can join the Julia Slack channel following instructions here: https://discourse.julialang.org/t/announcing-a-julia-slack/4866

[flystar233]

There are so many dependency packages that I don't think it's all useful. The packages of julia still have too many deadly bugs in the repair process, such as building and network connections. Using R or Python might be a wise choice

[gtollefson]

@flystar233 Can you tell me specifically what your errors are?

Our dependency builds are all passing and we perform cross platform testing on macOS, Windows, and Linux operating systems.

Please tell me what operating system and Julia version you are using. Additionally, since you mention network connections, tell me if you are installing Julia packages on a shared network with firewalls or on a remote server. Please post the complete error messages that you receive when trying to install VariantVisualization.jl and when building any broken dependencies.

We carefully chose to build VIVA using Julia language, rather than Python or R, for a variety of reasons including its power, efficiency, and growing popularity in data science and biology research. You can read more about why we chose to use Julia by reading our preprint here: https://www.biorxiv.org/content/10.1101/589879v1

[flystar233]

Thank you for your patience. My operating system is Win10 and Julia version is 1.0.3 (I tried version 1.1.0 too). There are several mistakes: Pkg.build("Rsvg") building LibCURL LibCURL wanted to download some packages according to bulid.jl, but there was no response. I chacked the bulid.jl, and manually downloaded these packages by chrome. I have no idea that why does this happen and where should these packages be put? building WinRPM was also no response.

[gtollefson]

@flystar233 I’m happy to help and very glad you are interested in using our tool 😊.

I’m confused by your description of the error messages. Can you copy and paste the complete error messages from your command line output?

Please include all error messages you receive when you: 1) clone VariantVisualization.jl and 2) build any broken packages

[flystar233]

I can't download the files required by LibCURL, which may be due to some reasons. I can't solve this problem. Can you give me the entire folder of LibCURL and WinRPM? I'd like to replace my files with them and try again.

[gtollefson]

@flystar233

Rsvg builds (along with LibCURL and WinRPM) on Windows 10 64 and 32 bit for me. I recommend sharing your error messages and system configurations on the following package issues pages:

https://github.com/JuliaWeb/LibCURL.jl/issues https://github.com/JuliaPackaging/WinRPM.jl/issues

It looks like this may be an issue with BinaryProvider. Here's a similar error with a fix, for a different package. https://github.com/JuliaOpt/Clp.jl/issues/38

You could reference this issue https://github.com/JuliaOpt/Clp.jl/issues/38 as it may be relevant.

[gtollefson]

@flystar233 Were you able to set up and use VIVA?

[gtollefson]

@flystar233 I'm going to close this, but please feel free to ask any questions here in the future.

[gtollefson]

@flystar233 We've developed a Docker container to run VIVA. This way, you won't have to install Julia or Julia package dependencies to run the tool. You just need to install Docker - check out our new installation docs