From 4786d3cce66a99934529fa6c1b491f4b960cebc0 Mon Sep 17 00:00:00 2001 From: John Huddleston Date: Wed, 30 Aug 2023 10:39:06 -0700 Subject: [PATCH] Bump versions for Nextstrain tools in Conda env Bumps versions for Augur, Nextalign, and Nextclade along with Python. We can't use Python 3.9 or higher with this environment file, since the pinned versions of pangolin require older versions of dependencies that aren't compatible with Python 3.9 or higher. In future updates, we could either bump pangolin and pangolearn and/or define pangolin dependencies in their own environment file and use that file in the workflow's few pangolin rules. This latter option is probably better, since it simplifies the default environment (speeding up its installation, reducing its size) and still supports pangolin in the workflow with Snakemake's `--use-conda` interface. --- workflow/envs/nextstrain.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/workflow/envs/nextstrain.yaml b/workflow/envs/nextstrain.yaml index c2b1ce23a..080c872f1 100644 --- a/workflow/envs/nextstrain.yaml +++ b/workflow/envs/nextstrain.yaml @@ -4,11 +4,11 @@ channels: - bioconda - defaults dependencies: - - augur=22.0.1 + - augur=22.4.0 - epiweeks=2.1.2 - iqtree=2.2.0.3 - - nextalign=2.13.1 - - nextclade=2.13.1 + - nextalign=2.14.0 + - nextclade=2.14.0 - pangolin=3.1.20 - pangolearn=2022.01.20 - - python>=3.7* + - python>=3.8*