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Author: DaanJansen94

conda-recipes/meta.yaml

@@ -0,0 +1,62 @@
+{% set name = "recmpox" %}
+{% set version = "0.0.1" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/DaanJansen94/RecMpox/archive/v{{ version }}.tar.gz
+  sha256: 1ff173a14df65d214d7a3b57b14f2442414680ad95629c07490cf28e7923c2c5
+
+build:
+  number: 0
+  noarch: python
+  entry_points:
+    - recmpox=recmpox.recmpox:main
+  script:
+    - "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv"
+    - mkdir -p $PREFIX/etc/conda/activate.d $PREFIX/etc/conda/deactivate.d
+    - echo 'export PYTHONNOUSERSITE=1' > $PREFIX/etc/conda/activate.d/recmpox-env-vars.sh
+    - echo 'unset PYTHONNOUSERSITE' > $PREFIX/etc/conda/deactivate.d/recmpox-env-vars.sh
+  run_exports:
+    - {{ pin_subpackage(name, max_pin='x.x') }}
+
+requirements:
+  host:
+    - python >=3.9
+    - pip
+    - setuptools
+  run:
+    - python >=3.9
+    - minimap2
+    - samtools
+    - squirrel
+
+test:
+  imports:
+    - recmpox
+  commands:
+    - recmpox --help
+
+about:
+  home: https://github.com/DaanJansen94/RecMpox
+  license: GPL-3.0-or-later
+  license_family: GPL
+  license_file: LICENSE
+  summary: RecMpox flags potential recombination events in monkeypox consensus genomes.
+  description: |
+    When the environment is activated, PYTHONNOUSERSITE=1 is set so Squirrel and RecMpox use only the conda env's packages.
+    RecMpox is a command-line tool that flags potential recombination events in monkeypox viruses.
+    It identifies recombination tract breakpoints within your own provided consensus genomes.
+    It does not confirm recombination; it flags genomes that may be recombinant for further investigation.
+    RecMpox takes two references (e.g. Clade Ia vs Ib, or IIa vs IIb), aligns them with Squirrel,
+    finds diagnostic SNP positions where the references differ, then classifies each consensus genome
+    at those positions. Genomes where both refs contribute at least 5% are flagged as potential
+    recombinants; recombination tracts and breakpoints are inferred along the genome.
+  doc_url: https://github.com/DaanJansen94/RecMpox/blob/main/README.md
+  dev_url: https://github.com/DaanJansen94/RecMpox
+
+extra:
+  recipe-maintainers:
+    - DaanJansen94