From b21688dee43c103394f75bfdab68390221896fda Mon Sep 17 00:00:00 2001 From: Angie Hinrichs Date: Mon, 16 Jun 2025 12:34:54 -0700 Subject: [PATCH 1/3] Add entries for pangolin-data/-assignment 1.34 --- pangolin/data/data_compatibility.csv | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pangolin/data/data_compatibility.csv b/pangolin/data/data_compatibility.csv index bd7dcf2..0ae578b 100644 --- a/pangolin/data/data_compatibility.csv +++ b/pangolin/data/data_compatibility.csv @@ -1,4 +1,5 @@ data_source,version,min_pangolin_version,min_scorpio_version +pangolin-data,1.34,4.3, pangolin-data,1.33,4.3, pangolin-data,1.32,4.3, pangolin-data,1.31,4.3, @@ -32,6 +33,7 @@ pangolin-data,1.6,4, pangolin-data,1.3,4, pangolin-data,1.2.133,4, pangolin-data,1.2.127,4, +pangolin-assignment,1.34,4.3, pangolin-assignment,1.33,4.3, pangolin-assignment,1.32,4.3, pangolin-assignment,1.31,4.3, From 27b15f4cbba7facb07f6476604e053d84991db1d Mon Sep 17 00:00:00 2001 From: Angie Hinrichs Date: Thu, 11 Sep 2025 12:12:47 -0700 Subject: [PATCH 2/3] Add entries for pangolin-data/-assignment 1.35 --- pangolin/data/data_compatibility.csv | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pangolin/data/data_compatibility.csv b/pangolin/data/data_compatibility.csv index 0ae578b..ee43b44 100644 --- a/pangolin/data/data_compatibility.csv +++ b/pangolin/data/data_compatibility.csv @@ -1,4 +1,5 @@ data_source,version,min_pangolin_version,min_scorpio_version +pangolin-data,1.35,4.3, pangolin-data,1.34,4.3, pangolin-data,1.33,4.3, pangolin-data,1.32,4.3, @@ -33,6 +34,7 @@ pangolin-data,1.6,4, pangolin-data,1.3,4, pangolin-data,1.2.133,4, pangolin-data,1.2.127,4, +pangolin-assignment,1.35,4.3, pangolin-assignment,1.34,4.3, pangolin-assignment,1.33,4.3, pangolin-assignment,1.32,4.3, From d57ae0800f6a9a6cd5a9447b97007a6dd4f35ce6 Mon Sep 17 00:00:00 2001 From: Angie Hinrichs Date: Thu, 11 Sep 2025 14:45:24 -0700 Subject: [PATCH 3/3] Constrain usher version to be 0.6.5 or lower because bioconda version 0.6.6 seems broken (lineage A assigned to all sequences). --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index d60271e..a163b54 100644 --- a/environment.yml +++ b/environment.yml @@ -11,7 +11,7 @@ dependencies: - snakemake-minimal=7.24.0 - gofasta - ucsc-fatovcf>=426 - - usher>=0.5.4 + - usher>=0.5.4,<=0.6.5 - git-lfs - pip: - git+https://github.com/cov-lineages/pangolin-data.git