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Add get_mnv #51178

Merged
merged 13 commits into from
Oct 7, 2024
Merged

Add get_mnv #51178

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dce5aa4
add get_mnv
Paururo Oct 5, 2024
64c730c
add get_mnv
Paururo Oct 5, 2024
eeeaa3a
Fix typo, add categories
Paururo Oct 5, 2024
1dcc3da
Add run_exports to get_mnv recipe
Paururo Oct 5, 2024
48bb441
fix run_exports to get_mnv recipe
Paururo Oct 5, 2024
60b8600
fix dependencies
Paururo Oct 5, 2024
628d818
fix dependencies
Paururo Oct 5, 2024
2a25e4a
fix open error
Paururo Oct 5, 2024
7ad6edb
try connect
Paururo Oct 5, 2024
308fc05
Update license
Paururo Oct 6, 2024
3770d9c
libraries to host and add license_fam
Paururo Oct 6, 2024
17df3f1
libraries to host and add license_fam
Paururo Oct 6, 2024
c2af868
add rabit sugg pins in run, license and ver
Paururo Oct 6, 2024
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71 changes: 71 additions & 0 deletions recipes/get_mnv/meta.yaml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,71 @@
{% set name = "get_mnv" %}
{% set version = "1.0.0" %}
{% set sha256 = "b9ba6fe1a5f5f73afa98cde9e348f7861d44690f795338816a8a0724a66e1aa8" %}

package:
name: "{{ name|lower }}"
version: "{{ version }}"

source:
url: "https://github.com/PathoGenOmics-Lab/{{ name }}/archive/refs/tags/{{ version }}.tar.gz"
sha256: "{{ sha256 }}"

build:
number: 0
script: |
export LANG=C.UTF-8
export LC_ALL=C.UTF-8
export RUST_BACKTRACE=1
export OPENSSL_NO_VENDOR=1
export OPENSSL_DIR=$PREFIX
export OPENSSL_INCLUDE_DIR=$PREFIX/include
export OPENSSL_LIB_DIR=$PREFIX/lib
export CURL_STATIC_SSL=1
export CURL_SYS_STATIC=1
#export CARGO_NET_OFFLINE=true
export HTS_LIB_DIR=$PREFIX/lib
export HTS_INCLUDE_DIR=$PREFIX/include
export HTS_STATIC=1
export HTS_SYS_BUNDLED=0
cargo install --no-track --locked --verbose --root "${PREFIX}" --path .
run_exports:
- {{ pin_subpackage(name, max_pin="x") }}

requirements:
build:
- {{ compiler('rust') }}
- openssl
- curl
- pkg-config
- htslib
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The libraries should be in 'host', not 'build'

- bzip2
- xz
- zlib
run:
- openssl
- curl
- htslib
- bzip2
- xz
- zlib
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🛠️ Refactor suggestion

Refactor suggestion: Adjust requirements section structure.

Consider restructuring the requirements section to better align with Bioconda best practices:

  1. Move the libraries (openssl, curl, htslib, bzip2, xz, zlib) from the 'build' section to a new 'host' section.
  2. Keep only the Rust compiler and pkg-config in the 'build' section.
  3. Adjust the 'run' section to use the {{ pin_compatible() }} function for the libraries.

Here's a suggested restructure:

requirements:
  build:
    - {{ compiler('rust') }}
    - pkg-config
  host:
    - openssl
    - curl
    - htslib
    - bzip2
    - xz
    - zlib
  run:
    - {{ pin_compatible('openssl') }}
    - {{ pin_compatible('curl') }}
    - {{ pin_compatible('htslib') }}
    - {{ pin_compatible('bzip2') }}
    - {{ pin_compatible('xz') }}
    - {{ pin_compatible('zlib') }}

This structure ensures that the libraries are available at build time and properly pinned at runtime.


test:
commands:
- get_mnv --help
Comment on lines +55 to +57
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🛠️ Refactor suggestion

Enhance test coverage.

While the current test ensures that the get_mnv binary is installed and executable, consider adding more comprehensive tests to verify the tool's functionality. For example:

test:
  commands:
    - get_mnv --help
    - get_mnv --version
    - get_mnv --test  # If there's a built-in test option
    # Add a command to run get_mnv on a small test dataset, if possible

These additional tests would provide better assurance that the tool is functioning correctly after installation.

Would you like assistance in generating more specific test commands based on the tool's functionality?


about:
home: "https://github.com/PathoGenOmics-Lab/get_mnv"
license: "GPL-3.0-or-later"
license_file: LICENSE
summary: "Tool to identify Multi-Nucleotide Variants (MNVs) in genomic sequences."
description: |
get_MNV is a tool designed to identify Multi-Nucleotide Variants (MNVs) within the same codon in genomic sequences, providing more accurate annotation for genomic data.
doc_url: "https://github.com/PathoGenOmics-Lab/get_mnv"
dev_url: "https://github.com/PathoGenOmics-Lab/get_mnv"
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⚠️ Potential issue

Update license specification and LGTM for the rest.

The about section provides comprehensive information about the package. However, please update the license specification as per a previous review comment:

-  license: "GPL-3.0-or-later"
+  license: "GPL-3.0"
+  license_family: GPL3

This change ensures consistency with Bioconda's preferred license specification format.

The rest of the section, including the home page, summary, description, and URLs, is well-defined and informative.

📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
about:
home: "https://github.com/PathoGenOmics-Lab/get_mnv"
license: "GPL-3.0-or-later"
license_file: LICENSE
summary: "Tool to identify Multi-Nucleotide Variants (MNVs) in genomic sequences."
description: |
get_MNV is a tool designed to identify Multi-Nucleotide Variants (MNVs) within the same codon in genomic sequences, providing more accurate annotation for genomic data.
doc_url: "https://github.com/PathoGenOmics-Lab/get_mnv"
dev_url: "https://github.com/PathoGenOmics-Lab/get_mnv"
about:
home: "https://github.com/PathoGenOmics-Lab/get_mnv"
license: "GPL-3.0"
license_family: GPL3
license_file: LICENSE
summary: "Tool to identify Multi-Nucleotide Variants (MNVs) in genomic sequences."
description: |
get_MNV is a tool designed to identify Multi-Nucleotide Variants (MNVs) within the same codon in genomic sequences, providing more accurate annotation for genomic data.
doc_url: "https://github.com/PathoGenOmics-Lab/get_mnv"
dev_url: "https://github.com/PathoGenOmics-Lab/get_mnv"


extra:
recipe-maintainers:
- PathoGenOmics-Lab
categories:
- Genomics
- Variant Analysis
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