From e7f636fcf1fb5d2aa800408a960fe7f4c4066636 Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Fri, 1 Nov 2024 00:57:33 +0100
Subject: [PATCH] Add Eagle2

---
 recipes/eagle2/build.sh  | 20 +++++++++++++++++++
 recipes/eagle2/meta.yaml | 43 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 63 insertions(+)
 create mode 100644 recipes/eagle2/build.sh
 create mode 100644 recipes/eagle2/meta.yaml

diff --git a/recipes/eagle2/build.sh b/recipes/eagle2/build.sh
new file mode 100644
index 0000000000000..cb2187de81f73
--- /dev/null
+++ b/recipes/eagle2/build.sh
@@ -0,0 +1,20 @@
+#!/bin/bash
+
+export COMMIT_VERS="${PKG_VERSION}"
+export COMMIT_DATE="$(date -Idate -u)"
+
+make \
+    -j 4 \
+    DYN_LIBS="-lz -lpthread -lbz2 -lblas" \
+    CXX="$CXX -std=c++17" \
+    CXXFLAG="$CXXFLAGS ${PREFIX} -D__COMMIT_ID__='\"${COMMIT_VERS}\"' -D__COMMIT_DATE__='\"${COMMIT_DATE}\"' \
+    LDFLAG="$LDFLAGS" \
+    HTSLIB_INC="$PREFIX" \
+    HTSLIB_LIB="-lhts" \
+    BOOST_INC="/usr/include"\
+    BOOST_LIB_IO="-lboost_iostreams" \
+    BOOST_LIB_PO="-lboost_program_options" \
+    BOOST_LIB_SE="-lboost_serialization" \
+    ;
+install "bin/eagle" "eagle/bin"
+popd
diff --git a/recipes/eagle2/meta.yaml b/recipes/eagle2/meta.yaml
new file mode 100644
index 0000000000000..1414afc24cf1f
--- /dev/null
+++ b/recipes/eagle2/meta.yaml
@@ -0,0 +1,43 @@
+{% set version = "2.4.1" %}
+
+package:
+  name: Eagle2
+  version: {{ version }}
+
+build:
+  number: 1
+
+source:
+  url: https://github.com/poruloh/Eagle/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 85804bfe972186ccb66e602856d6e04044302e5c0dbf9309849b0cde981e3432
+
+requirements:
+  build:
+    - make
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+  host:
+    - htslib >=1.9
+    - bzip2
+    - zlib
+    - boost-cpp >=1.58
+    - blas >= 0.2.19
+  run:
+    - boost-cpp
+
+test:
+  commands:
+    - eagle --help
+
+about:
+  home: https://github.com/poruloh/Eagle
+  license: GPLv3
+  summary: The Eagle software estimates haplotype phase either within a genotyped cohort or using a phased reference panel.
+  description:
+    Eagle2 is now the default phasing method used by the Sanger and Michigan imputation servers and uses a new
+    very fast HMM-based algorithm that improves speed and accuracy over existing methods via two key ideas;
+    a new data structure based on the positional Burrows-Wheeler transform and a rapid search algorithm that
+    explores only the most relevant paths through the HMM. Compared to the Eagle1 algorithm, Eagle2 has similar
+    speed but much greater accuracy at sample sizes <50,000; as such, we have made the Eagle2 algorithm the default option.
+    (The Eagle1 algorithm can be accessed via the --v1 flag.) Eagle v2.3+ supports phasing sequence data with or without
+    a reference and also supports phasing chrX.
\ No newline at end of file