Upgrade to version 3.0 #291
Conversation
Hi @nickjcroucher, I have installed Gubbins in Ubuntu based on the instructions in the manual, but it is still in the 1.2.4 version and I encountered memory resource issues. Can you please provide the instructions on how I can upgrade to the latest version of Gubbins? Thank you and Happy New Year! Kind Regards, |
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Hi @degreesKelvin - I would not recommend using v3.0.0 yet, as we have not validated the accuracy of the results (coming soon hopefully!) - in the first instance, I would try installing the latest version available on conda (v2.4.1), which has some fixes to memory usage (it also uses marginal ancestral reconstruction, which may not be as accurate as the joint ancestral reconstruction in v1.2.4, but is likely to be faster and more memory efficient). If v2.4.1 doesn't work either, let me know - hopefully v3.0 will be ready for wider use soon! |
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Thank you Nick!
It is showing the correct version now:
run_gubbins.py --version
2.4.1
Kind Regards,
Kelvin 😊
From: nickjcroucher <notifications@github.com>
Sent: Friday, 15 January 2021 4:59 PM
To: sanger-pathogens/gubbins <gubbins@noreply.github.com>
Cc: Kelvin Leong <kelvin.leong@utas.edu.au>; Mention <mention@noreply.github.com>
Subject: Re: [sanger-pathogens/gubbins] Upgrade to version 3.0 (#291)
Hi @degreesKelvin<https://github.com/degreesKelvin> - I would not recommend using v3.0.0 yet, as we have not validated the accuracy of the results (coming soon hopefully!) - in the first instance, I would try installing the latest version available on conda (v2.4.1), which has some fixes to memory usage (it also uses marginal ancestral reconstruction, which may not be as accurate as the joint ancestral reconstruction in v1.2.4, but is likely to be faster and more memory efficient). If v2.4.1 doesn't work either, let me know - hopefully v3.0 will be ready for wider use soon!
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Makefile removed in 2377005. |
Happy new year! Addresses most of the improvements discussed in #1. CI switched to Github Actions and currently passing all tests on Linux and OSX. Just restructuring of the code and packaging to address, which seems easier to deal with post-PR.