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yekaizhou / duet

SNP-Assisted SV Calling and Phasing Using ONT
BSD 3-Clause "New" or "Revised" License
23 stars 2 forks source link

Request: A docker image with duet #13

Open haraldgrove opened 1 year ago

haraldgrove commented 1 year ago

Hi

While this program looks quite promising, we're encountering several problems trying to install the required software to make duet run.

Would it be possible to provide a docker image with duet and its runtime environment?

-Harald

yekaizhou commented 1 year ago

Hi Harald,

Many thanks for using Duet. Duet has a unique feature to phase SVs so that it requires many additional dependencies to make it happen. Sometimes the environment may fail to solve, especially when there are many packages installed.

Could you please try create a separate clean env and install duet? It may also take a while to complete.

Let me know if you have other questions.

Thanks, Yekai

jamesdalg commented 1 year ago

I will agree that your package is unique and offers something that no other package on the market has-- phasing for long read callers besides pbsv. It is an excellent tool-- no lie. But, having made a package with 129 dependencies that was difficult for others to install a few years ago... I get where he is coming from. I think a docker package could really help adoption. deepvariant and nanocaller both use this to help their userbase. It would go a long way to making your program more used, and eliminate your need to update it. I think it will help all parties involved. I'll try to make one, but I have my own errors with clair3 I'm working through.

yekaizhou commented 1 year ago

@jamesdalg @haraldgrove Thank you for your interests in Duet. I will try to make a docker image.

@jamesdalg You can post your issue of Clair3 at https://github.com/HKU-BAL/Clair3/issues if you are also using Clair3. Duet and Clair3 are ran by the same lab.

Yekai