Add Eagle2 (#51851)

* Add Eagle2 * Fix linting * Fix scripts * Fix install * Improve build script * Update files * Set to dynamic * Fix directory * Fix sed command * Set -euo * Update example * Update meta.yml * Update meta.yml * Update meta.yml * Update meta.yml * Update meta.yml * Set version compiler * Update C++ version --------- Co-authored-by: Louis Le Nezet <[email protected]>
bioconda · Nov 4, 2024 · 3a3d558 · 3a3d558
1 parent b017356
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diff --git a/recipes/eagle2/0001-Use-CXX-and-flags.patch b/recipes/eagle2/0001-Use-CXX-and-flags.patch
@@ -0,0 +1,5 @@
+--- src/Makefile
++++ src/Makefile
+@@ -1,99 +1,99 @@
+-O = DipTreePBWT.o Eagle.o EagleImpMiss.o EagleParams.o EaglePBWT.o FileUtils.o GenoData.o HapHedge.o MapInterpolater.o MemoryUtils.o NumericUtils.o StaticMultimap.o StringUtils.o SyncedVcfData.o Timer.o memcpy.o
++O = DipTreePBWT.o Eagle.o EagleImpMiss.o EagleParams.o EaglePBWT.o FileUtils.o GenoData.o HapHedge.o MapInterpolater.o MemoryUtils.o NumericUtils.o StaticMultimap.o StringUtils.o SyncedVcfData.o Timer.o
diff --git a/recipes/eagle2/build.sh b/recipes/eagle2/build.sh
@@ -0,0 +1,33 @@
+#!/bin/bash
+
+set -euo pipefail
+
+echo "Building Eagle2 version ${PKG_VERSION}"
+
+cd src || exit 1
+
+sed -i.bak 's/memcpy.o//g' Makefile
+
+# Set up environment variables for building
+export BOOST_INSTALL_DIR=$PREFIX
+export HTSLIB_DIR=$PREFIX/lib
+export BLAS_DIR=$PREFIX/lib
+export ZLIB_STATIC_DIR=$PREFIX/lib
+
+# Run make
+make CC=${CXX} \
+    -e -j ${CPU_COUNT} \
+    CFLAGS="$CXXFLAGS -Wno-unused-result -std=c++11" \
+    BOOST_INSTALL_DIR=$BOOST_INSTALL_DIR \
+    HTSLIB_DIR=$HTSLIB_DIR \
+    BLAS_DIR=$BLAS_DIR \
+    ZLIB_STATIC_DIR=$ZLIB_STATIC_DIR \
+    LIBSTDCXX_STATIC_DIR=${PREFIX}/lib \
+    linking=dynamic
+
+echo "Installing Eagle2..."
+mkdir -p "${PREFIX}/bin"
+install -m 755 eagle "${PREFIX}/bin/"
+echo "Eagle2 installation completed successfully"
+
+cd .. || exit 1
diff --git a/recipes/eagle2/meta.yaml b/recipes/eagle2/meta.yaml
@@ -0,0 +1,49 @@
+{% set version = "2.4.1" %}
+
+package:
+  name: eagle2
+  version: {{ version }}
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('eagle2', max_pin='x.x.x') }}
+
+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
+    - openblas >=0.2.19
+  run:
+    - {{ pin_compatible('bzip2') }}
+    - {{ pin_compatible('zlib') }}
+    - {{ pin_compatible('boost-cpp') }}
+    - {{ pin_compatible('openblas') }}
+
+
+test:
+  commands:
+    - eagle -h
+
+about:
+  home: https://github.com/poruloh/Eagle
+  license: GPL-3.0-or-later
+  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.