From de330881b7bca45c85c1b8307659e9c374b583d4 Mon Sep 17 00:00:00 2001 From: Mark Bicknell Date: Thu, 17 Oct 2024 16:42:51 +0100 Subject: [PATCH 1/4] 0.8.2 changelog --- CHANGELOG.md | 12 ++++++++++++ README.md | 8 ++++---- 2 files changed, 16 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 26d4bce15..ba2ca8861 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,18 @@ All notable changes to Dorado will be documented in this file. +# [0.8.2] (21 Oct 2024) + +This release of Dorado includes fixes and improvements to the Dorado 0.8.1 release, including + +* 543ccc1a4b78c8d04960a769d03d1f61ca75d0e3 - Improve documentation on running dorado in PowerShell on Windows +* 3a8094a134dc448803c00aa93f6160c96241a9ab - Clarify "Unable to find chunk benchmarks" warning to indicate that it is not an error +* bac446937f5bc378ebf14169d7287b6e4c5b5efb - Fix error when passing invalid option to basecaller `--modified-bases` argument +* 7f40154aed13324865123386b278f3782eafa107 - Fix bug when running on GPUs with less than the recommended VRAM +* a993a32f6904991135ce14387740b0216b2136c9 - Prevent loss of small numbers of reads from `dorado correct` +* bbbeb9a72a79e77101f67dbab2a1c5f1cc4dd1d3 - Fix error when `dorado demux` is provided an empty input directory + + # [0.8.1] (3 Oct 2024) This release of Dorado includes fixes and improvements to the Dorado 0.8.0 release, including corrected configuration for DNA v5 SUP-compatible 5mC_5hmC and 5mCG_5hmCG models, improved cDNA poly(A) tail estimation for data from MinION flow cells, reduced basecaller startup time on supported GPUs, and more. diff --git a/README.md b/README.md index de392ce30..a1e1bf238 100644 --- a/README.md +++ b/README.md @@ -22,10 +22,10 @@ If you encounter any problems building or running Dorado, please [report an issu First, download the relevant installer for your platform: - - [dorado-0.8.1-linux-x64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.8.1-linux-x64.tar.gz) - - [dorado-0.8.1-linux-arm64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.8.1-linux-arm64.tar.gz) - - [dorado-0.8.1-osx-arm64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.8.1-osx-arm64.zip) - - [dorado-0.8.1-win64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.8.1-win64.zip) + - [dorado-0.8.2-linux-x64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.8.2-linux-x64.tar.gz) + - [dorado-0.8.2-linux-arm64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.8.2-linux-arm64.tar.gz) + - [dorado-0.8.2-osx-arm64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.8.2-osx-arm64.zip) + - [dorado-0.8.2-win64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.8.2-win64.zip) Once the relevant `.tar.gz` or `.zip` archive is downloaded, extract the archive to your desired location. From da53e955cf0bdbb6dc2eb0332c4686b2cb40e198 Mon Sep 17 00:00:00 2001 From: Mark Bicknell Date: Thu, 17 Oct 2024 16:44:29 +0100 Subject: [PATCH 2/4] fix typo in changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ba2ca8861..5fe8d3431 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,7 +4,7 @@ All notable changes to Dorado will be documented in this file. # [0.8.2] (21 Oct 2024) -This release of Dorado includes fixes and improvements to the Dorado 0.8.1 release, including +This release of Dorado includes fixes and improvements to the Dorado 0.8.1 release. * 543ccc1a4b78c8d04960a769d03d1f61ca75d0e3 - Improve documentation on running dorado in PowerShell on Windows * 3a8094a134dc448803c00aa93f6160c96241a9ab - Clarify "Unable to find chunk benchmarks" warning to indicate that it is not an error From 6f5f21e2c2f222a4a1f1a04f45ee5f53cf233160 Mon Sep 17 00:00:00 2001 From: Mark Bicknell Date: Thu, 17 Oct 2024 17:21:57 +0100 Subject: [PATCH 3/4] Add missing entry to 0.8.2 changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5fe8d3431..827cb9470 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,7 @@ All notable changes to Dorado will be documented in this file. This release of Dorado includes fixes and improvements to the Dorado 0.8.1 release. +* 9a81cbc269b742cad64b514a50aeb30a7bf25811 - Fix errors when running `dorado basecaller` on multi-gpu systems * 543ccc1a4b78c8d04960a769d03d1f61ca75d0e3 - Improve documentation on running dorado in PowerShell on Windows * 3a8094a134dc448803c00aa93f6160c96241a9ab - Clarify "Unable to find chunk benchmarks" warning to indicate that it is not an error * bac446937f5bc378ebf14169d7287b6e4c5b5efb - Fix error when passing invalid option to basecaller `--modified-bases` argument From 8791a228d0fbc120d020e7080040e083dcf50700 Mon Sep 17 00:00:00 2001 From: Susie Lee Date: Thu, 17 Oct 2024 17:41:57 +0100 Subject: [PATCH 4/4] Changelog reorder --- CHANGELOG.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 827cb9470..d582b5424 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,13 +6,13 @@ All notable changes to Dorado will be documented in this file. This release of Dorado includes fixes and improvements to the Dorado 0.8.1 release. -* 9a81cbc269b742cad64b514a50aeb30a7bf25811 - Fix errors when running `dorado basecaller` on multi-gpu systems -* 543ccc1a4b78c8d04960a769d03d1f61ca75d0e3 - Improve documentation on running dorado in PowerShell on Windows -* 3a8094a134dc448803c00aa93f6160c96241a9ab - Clarify "Unable to find chunk benchmarks" warning to indicate that it is not an error +* 9a81cbc269b742cad64b514a50aeb30a7bf25811 - Fix errors when running `dorado basecaller` on multi-GPU systems * bac446937f5bc378ebf14169d7287b6e4c5b5efb - Fix error when passing invalid option to basecaller `--modified-bases` argument * 7f40154aed13324865123386b278f3782eafa107 - Fix bug when running on GPUs with less than the recommended VRAM * a993a32f6904991135ce14387740b0216b2136c9 - Prevent loss of small numbers of reads from `dorado correct` * bbbeb9a72a79e77101f67dbab2a1c5f1cc4dd1d3 - Fix error when `dorado demux` is provided an empty input directory +* 3a8094a134dc448803c00aa93f6160c96241a9ab - Clarify "Unable to find chunk benchmarks" warning to indicate that it is not an error +* 543ccc1a4b78c8d04960a769d03d1f61ca75d0e3 - Improve documentation on running Dorado in PowerShell on Windows # [0.8.1] (3 Oct 2024)