From 8ea059ff13019c023804434b70144ac6ff8f9516 Mon Sep 17 00:00:00 2001
From: Andrea Manica <am315@cam.ac.uk>
Date: Fri, 27 Sep 2024 09:34:49 +0100
Subject: [PATCH] Add recipe for consensify (#50969)

* Add consensify recipe

* Complete about section

* small edits

* Edits following coderabbitai

* Add more advanced test

* Implement edits by @martin-g and remove complex test

mulled-test ignores resources set in the meta.yaml, so the more advanced tests that work on conda fail on mulled.
---
 recipes/consensify/build.sh  | 11 +++++++++++
 recipes/consensify/meta.yaml | 36 ++++++++++++++++++++++++++++++++++++
 2 files changed, 47 insertions(+)
 create mode 100755 recipes/consensify/build.sh
 create mode 100644 recipes/consensify/meta.yaml

diff --git a/recipes/consensify/build.sh b/recipes/consensify/build.sh
new file mode 100755
index 0000000000000..47b288b6ed904
--- /dev/null
+++ b/recipes/consensify/build.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+## compile
+${CXX} -c consensify_c.cpp -I./ ${CXXFLAGS}
+
+## link
+${CXX} consensify_c.o -o consensify_c -lz ${LDFLAGS}
+
+## install
+mkdir -p $PREFIX/bin
+cp consensify_c ${PREFIX}/bin/consensify_c
diff --git a/recipes/consensify/meta.yaml b/recipes/consensify/meta.yaml
new file mode 100644
index 0000000000000..615831e06e081
--- /dev/null
+++ b/recipes/consensify/meta.yaml
@@ -0,0 +1,36 @@
+{% set version = "2.4.0" %}
+
+package:
+  name: consensify
+  version: {{ version }}
+
+source:
+  url: https://github.com/jlapaijmans/Consensify/archive/refs/tags/{{ version }}.tar.gz
+  sha256: 2b88cda2c6ad44b6fd749d86485d3f16418b189b9c8ff4d20dd19640792dac1e
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('consensify', max_pin="x") }}
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+  host:
+    - zlib
+  run:
+    - zlib
+
+test:
+  commands:
+    - consensify_c -h
+
+about:
+  home: https://github.com/jlapaijmans/Consensify
+  license: GPL-3.0-or-later
+  license_family: GPL
+  license_file: LICENCE.txt
+  dev_url: https://github.com/jlapaijmans/Consensify
+  doc_url: https://github.com/jlapaijmans/Consensify
+  summary: A method for generating a consensus pseudohaploid genome sequence
+  about: Consensify is a method for generating a consensus pseudohaploid genome sequence with greatly reduced error rates compared to standard pseudohaploidisation. The method is described in full and tested in the associated publication (Barlow et al. (2020), Genes 11:50, doi 10.3390/genes11010050).