recipe.yaml

package:
  name: nextstrain-base
  version: "{{ environ['VERSION'] }}"

build:
  number: 0
  #
  # XXX TODO: If Boa ever supports conda-build's "pin_depends: strict" here¹, I
  # think it could replace our entire two-pass build process!  Unfortunately,
  # conda-build is so much slower than Boa that the more complicated build
  # process is worth it.
  #   -trs, 14 Oct 2022
  #
  # ¹ <https://github.com/mamba-org/boa/issues/300>
  #
  #pin_depends: strict

source:
  path: .

about:
  home: https://nextstrain.org
  doc_url: https://docs.nextstrain.org/
  dev_url: https://github.com/nextstrain/conda-base
  summary: Base Nextstrain runtime (meta-package)
  description: >
    This meta-package depends on all the other packages needed for a base
    Nextstrain runtime installed as a Conda environment.  As the
    nextstrain/base image is to Nextstrain CLI's Docker runtime, this
    nextstrain-base package is to Nextstrain CLI's Conda runtime.
  license: >
    The license for this meta-package is MIT; individual tools vary.

requirements:
  run:
    #
    # First-party
    #
    # XXX TODO: Include fauna?
    #
    - augur
    - auspice
    - evofr
    - nextalign
    - nextclade2
    - nextclade
    - nextstrain-cli
    - pathogen-embed

    #
    # Third-party
    #
    # XXX TODO: Pin some of these to the same versions the Docker runtime uses?
    # XXX TODO: No package available for Python envdir package.
    # XXX TODO: No package available for less.
    # XXX TODO: Omits pysam… but it may be unnecessary in the Docker runtime?
    # XXX TODO: Omits pango-designation… but it may be unnecessary in the Docker runtime?
    #
    # Include bash so that a newer version is guaranteed to be available on
    # systems with an older bash.  This is similar to how our Docker runtime
    # image includes its own bash too.
    #
    - awscli
    - bash
    - bzip2
    - csvtk
    - coreutils
    - curl
    - epiweeks
    - git
    - gawk
    - google-cloud-storage
    - grep
    - gzip
    - iqtree >=2
    - jq
    - ncbi-datasets-cli
    - pango_aliasor
    - perl
      # 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
    - xlrd
    - xz
    - zip
    - zstd

    # Avoid a newer minimum glibc version introduced by c-ares 1.33.0¹.  This
    # pin keeps the previous glibc requirement of ≥2.17 instead of ≥2.28.²
    # Eventually this pin will become unworkable, but we can keep it for now.
    #
    # Note that using run_constrained doesn't work (at least on the face of
    # it), potentially (?) because of our two-step build process.
    #   -trs, 16 Sept 2024
    #
    # ¹ <https://github.com/conda-forge/c-ares-feedstock/pull/38>
    # ² <https://github.com/nextstrain/conda-base/issues/92>
    - c-ares <1.33.0