From fc2688d63e47cd16c1dd9fd2af770cb2bbc21fa1 Mon Sep 17 00:00:00 2001
From: MarkStreek <90258835+MarkStreek@users.noreply.github.com>
Date: Thu, 2 Jan 2025 14:54:05 +0100
Subject: [PATCH] Add pacini_typing (#53012)

* add pacini_typing

* updated valid run exports

* fixed a very stupid typo in the run exports

* Update recipes/pacini_typing/meta.yaml

Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com>

* fixed some suggestions from code review

---------

Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com>
---
 recipes/pacini_typing/meta.yaml | 51 +++++++++++++++++++++++++++++++++
 1 file changed, 51 insertions(+)
 create mode 100644 recipes/pacini_typing/meta.yaml

diff --git a/recipes/pacini_typing/meta.yaml b/recipes/pacini_typing/meta.yaml
new file mode 100644
index 0000000000000..07b1ef0121072
--- /dev/null
+++ b/recipes/pacini_typing/meta.yaml
@@ -0,0 +1,51 @@
+{% set name = "pacini_typing" %}
+{% set version = "1.6.1" %}
+
+package:
+  name: "{{ name }}"
+  version: "{{ version }}"
+
+source:
+  url: https://github.com/RIVM-bioinformatics/Pacini-typing/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: f4bbd7daf83aa50e7de113ab55fb485eeba8e567fac6d48f5799e073a629d8b5
+
+build:
+  number: 0
+  noarch: python
+  script:
+    - {{ PYTHON }} -m pip install . --no-deps -vv
+  run_exports:
+    - {{ pin_subpackage("pacini_typing", max_pin="x") }}
+
+requirements:
+  host:
+    - python >=3.10,<=3.12
+    - pip
+  run:
+    - python >=3.10,<=3.12
+    - biopython
+    - pysam
+    - pyyaml
+    - networkx
+    - scipy
+    - numpy
+    - tqdm
+    - pandas
+    - blast
+    - kma
+
+test:
+  commands:
+    - pacini_typing --help
+    - Pacini-typing --help
+
+about:
+  home: "https://github.com/RIVM-bioinformatics/Pacini-typing"
+  license: AGPL-3.0
+  license_file: LICENSE
+  summary: "YAML-based bacterial genotyping application"
+  dev_url: "https://github.com/RIVM-bioinformatics/Pacini-typing"
+
+extra:
+  recipe-maintainers:
+    - MarkStreek