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Provide GNU awk, grep, sed, and tar in the runtime
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They're provided in our other runtimes (almost by happenstance, as part
of the underlying OS image) and having them available in all runtimes
makes it much easier to write portable programs without having to deal
with GNU vs. BSD differences.

Note that typically these GNU programs would already be available in the
Conda runtime on Linux (via the host system), but not the Conda runtime
on macOS (unless installed separately, e.g. via Homebrew).  So
explicitly including the GNU-flavored programs here increases
consistency, isolation, and portability of the runtime.

These were ostensibly overlooked in "Provide GNU coreutils in the
runtime" (a0b6609).

Related-to: <nextstrain/oropouche#18 (comment)>
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tsibley committed Oct 9, 2024
1 parent 5ac0316 commit 961e81b
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4 changes: 4 additions & 0 deletions src/recipe.yaml
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Expand Up @@ -68,7 +68,9 @@ requirements:
- curl
- epiweeks
- git
- gawk
- google-cloud-storage
- grep
- gzip
- iqtree >=2
- jq
Expand All @@ -78,9 +80,11 @@ requirements:
# Pin pulp <2.8 for snakemake: https://github.com/snakemake/snakemake/issues/2607
- pulp <2.8
- ruby
- sed
- seqkit
- snakemake <8
- sqlite
- tar
- tsv-utils
- unzip
- wget
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