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add r-chromvarmotifs #51395

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merged 4 commits into from
Oct 15, 2024
Merged

add r-chromvarmotifs #51395

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b1eee89
add r-chromvarmotifs
mfansler Oct 15, 2024
2879a04
add build.sh
mfansler Oct 15, 2024
265b339
include R 4.1
mfansler Oct 15, 2024
f997084
hash
mfansler Oct 15, 2024
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4 changes: 4 additions & 0 deletions recipes/r-chromvarmotifs/build.sh
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#!/bin/bash
export DISABLE_AUTOBREW=1
# shellcheck disable=SC2086
${R} CMD INSTALL --build . ${R_ARGS}
4 changes: 4 additions & 0 deletions recipes/r-chromvarmotifs/conda_build_config.yaml
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r_base:
- 4.1
- 4.2
- 4.3
45 changes: 45 additions & 0 deletions recipes/r-chromvarmotifs/meta.yaml
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{% set version = "0.2.0" %}
{% set github = "https://github.com/GreenleafLab/chromVARmotifs" %}
{% set commit = "38bed559c1f4770b6c91c80bf3f8ea965da26076" %}

package:
name: r-chromvarmotifs
version: "{{ version }}"

source:
url: "{{ github }}/archive/{{ commit }}.zip"
sha256: 4e3bd3201bb4680d78e7786a6c85af06f935a3be8117a87ef03ba375926ebe74

build:
noarch: generic
number: 0
rpaths:
- lib/R/lib/
- lib/
run_exports:
- {{ pin_subpackage("r-chromvarmotifs", max_pin="x.x") }}

requirements:
host:
- r-base
- bioconductor-tfbstools
run:
- r-base
- bioconductor-tfbstools
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🛠️ Refactor suggestion

Consider pinning the r-base version.

The requirements section includes the necessary dependencies. However, to ensure compatibility and reproducibility, it's recommended to pin the r-base version.

Consider updating the r-base requirement to specify a version range. For example:

requirements:
  host:
    - r-base {{ r_base }}
    - bioconductor-tfbstools
  run:
    - r-base {{ r_base }}
    - bioconductor-tfbstools

This assumes that {{ r_base }} is defined in your conda_build_config.yaml file. If not, you may need to specify the version explicitly, e.g., r-base >=4.1,<4.4.


test:
commands:
- $R -e "library(chromVARmotifs)"
Comment on lines +30 to +32
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🛠️ Refactor suggestion

Consider adding more comprehensive tests.

The current test command checks if the package can be loaded, which is a good basic test. However, to ensure the package functions correctly, consider adding more comprehensive tests.

You could add additional test commands to verify specific functionalities of the package. For example:

test:
  commands:
    - $R -e "library(chromVARmotifs)"
    - $R -e "stopifnot(length(chromVARmotifs::JASPAR2022_human) > 0)"
    - $R -e "stopifnot(is(chromVARmotifs::JASPAR2022_human, 'PWMatrixList'))"

These additional tests check if the package contains the expected data and if it's of the correct type.


about:
home: {{ github }}
license: MIT
license_family: MIT
license_file:
- {{ environ["PREFIX"] }}/lib/R/share/licenses/MIT
- LICENSE
summary: Stores several motifs as PWMatrixList objects for use in R with packages like motifmatchr and chromVAR.

extra:
recipe-maintainers:
- mfansler