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Illumina / hap.py

Haplotype VCF comparison tools
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python 2.x Sunset, potential 3.x port? #151

Open OsborneACollin opened 2 years ago

OsborneACollin commented 2 years ago

I have performed validation of the tools using python 2.7.18 with all of the required packages and am happy with how it all works.

With the python 2.x sunsetting having already taken place in 2020 and the 2.7.18 being the last update, we are concerned with any potential security vulnerabilities with python 2.x down the line.

Does Illumina have any plans on an official python 3.x port of hap.py? If not, is anyone aware of any successful ports of hap.py to 3.x that exist?

Thanks!

NateRMattson commented 2 years ago

We have been having the same discussion internally regarding the python version required. I also sent a note to illumina tech support to gather their thoughts.

dskola commented 2 years ago

Thanks for bringing this to our attention! This is something we've been considering for a while -- and now that V2 is over a year past EoL it's probably time. We hope to have an update in the next month or so.

OsborneACollin commented 2 years ago

@dskola That is fantastic to hear! We look forward to checking back in for those updates.

NateRMattson commented 2 years ago

@dskola Yes. Thank you for the update!

serge2016 commented 2 years ago

It would be great to see such port!

bsnewell commented 2 years ago

Hi, newbie question. Are you guys running hap.py using python 2.7, or converting with 2to3. Or using some other method to get it to install and run?

serge2016 commented 2 years ago

Dear @dskola, any news about the update?

sunnycxh commented 2 years ago

@serge2016 , we've discussed about the plans for hap.py and some investigation to migrate it to python 3. Unfortunately there is no allocation to complete the migration. To mitigate this, one solution would be to create a docker file with python 2 in the environment. Would this be a possible solution?