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Add recipe for snpick #52144

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merged 2 commits into from
Nov 19, 2024
Merged

Add recipe for snpick #52144

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bccaf06
Add recipe for snpick
Paururo Nov 16, 2024
cff1c86
Merge branch 'master' into add-snpick-recipe
mencian Nov 18, 2024
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70 changes: 70 additions & 0 deletions recipes/snpick/meta.yaml
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Original file line number Diff line number Diff line change
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{% set name = "snpick" %}
{% set version = "1.0.0" %}
{% set sha256 = "6a5ae16a65c92c90ecf710c4d53afa0e3a76b7a43554c52e48cda843f7e20744" %}

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: |
set -xe
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=$PREFIX/lib
export LIBCLANG_PATH=$PREFIX/lib
export CPLUS_INCLUDE_PATH=$PREFIX/include
cargo install --locked --verbose --root "${PREFIX}" --path .
run_exports:
- {{ pin_subpackage(name, max_pin="x") }}

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

test:
commands:
- snpick --help
- snpick --version

Comment on lines +45 to +49
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🛠️ Refactor suggestion

Enhance test coverage with functional tests.

Current tests only verify basic command availability. Consider adding functional tests:

test:
  commands:
    - snpick --help
    - snpick --version
+   # Add functional test with minimal example
+   - snpick --input test.fasta --output test.vcf
+  files:
+    - test.fasta

Would you like me to help create a minimal test dataset and corresponding test commands?

Committable suggestion skipped: line range outside the PR's diff.

about:
home: "https://github.com/PathoGenOmics-Lab/snpick"
license: "GPL-3.0-or-later"
license_family: GPL3
license_file: LICENSE
summary: "A fast and memory-efficient tool for SNP extraction from genomic alignments."
description: |
snpick is a Rust-based tool designed for extracting SNPs efficiently from large genomic alignments, with minimal RAM usage and high performance. It outputs variable sites in alignment files and provides VCF generation.
doc_url: "https://github.com/PathoGenOmics-Lab/snpick"
dev_url: "https://github.com/PathoGenOmics-Lab/snpick"

extra:
additional-platforms:
- linux-aarch64
- osx-arm64
recipe-maintainers:
- PathoGenOmics-Lab
categories:
- Genomics
- Variant Analysis
- SNP Extraction