From b290faea0e39d6fed6baa3b561e01e38d16a6c23 Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Thu, 25 Jan 2024 15:34:37 -0800 Subject: [PATCH] ambient-setup: Add csvtk, seqkit, and tsv-utils MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Prompted by https://github.com/nextstrain/measles/pull/10#discussion_r1465761518 These have become common commands used across Nextstrain pathogen repos¹ since they were added to the Docker runtime² ¹ https://github.com/search?q=org%3Anextstrain+AND+%28%22csvtk%22+OR+%22tsv-select%22+OR+%22seqkit%22%29&type=code ² https://github.com/nextstrain/docker-base/commit/992c575afa14e2b48b87d344a4643d6ff28f98d8 --- src/snippets/ambient-setup.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/snippets/ambient-setup.rst b/src/snippets/ambient-setup.rst index dcdd5589..eebd5421 100644 --- a/src/snippets/ambient-setup.rst +++ b/src/snippets/ambient-setup.rst @@ -12,7 +12,7 @@ -c conda-forge -c bioconda --yes \ augur auspice nextclade \ snakemake git epiweeks pangolin pangolearn \ - ncbi-datasets-cli + ncbi-datasets-cli csvtk seqkit tsv-utils 3. Set the runtime: