From dbb755557a08a38ee1387f136b05e44f973ebe64 Mon Sep 17 00:00:00 2001
From: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Date: Fri, 13 Dec 2024 12:41:12 +0200
Subject: [PATCH] Add a recipe for PopIns2

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
---
 recipes/popins2/build.sh      | 13 +++++++++
 recipes/popins2/meta.yaml     | 51 +++++++++++++++++++++++++++++++++++
 recipes/popins2/popins2.patch | 34 +++++++++++++++++++++++
 3 files changed, 98 insertions(+)
 create mode 100644 recipes/popins2/build.sh
 create mode 100644 recipes/popins2/meta.yaml
 create mode 100644 recipes/popins2/popins2.patch

diff --git a/recipes/popins2/build.sh b/recipes/popins2/build.sh
new file mode 100644
index 0000000000000..66dccd23a77a4
--- /dev/null
+++ b/recipes/popins2/build.sh
@@ -0,0 +1,13 @@
+#!/usr/bin/env bash
+
+set -xe
+
+# no need to build SeqAn's documentation/demos
+rm -rf external/seqan-library-2.2.0/share/doc/seqan/
+
+mkdir build
+
+CXX="${CXX} -std=c++14" make -j"${CPU_COUNT}"
+
+mkdir -p ${PREFIX}/bin
+install -m 755 popins2 ${PREFIX}/bin
diff --git a/recipes/popins2/meta.yaml b/recipes/popins2/meta.yaml
new file mode 100644
index 0000000000000..6a5c6a1176d08
--- /dev/null
+++ b/recipes/popins2/meta.yaml
@@ -0,0 +1,51 @@
+{% set name = "popins2" %}
+{% set version = "0.13.0" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage(name, max_pin='x.x') }}
+
+source:
+  git_url: https://github.com/kehrlab/PopIns2
+  git_rev: v{{ version }}
+  patches:
+    - popins2.patch
+
+requirements:
+  build:
+    - make
+    - {{ compiler('cxx') }}
+  host:
+    - bifrost
+    - bwa
+    - htslib
+    - samtools
+    - sickle-trim
+    - zlib
+  run:
+    - bifrost
+
+test:
+  commands:
+    - popins2 --help
+
+about:
+  home: https://github.com/kehrlab/PopIns2
+  license: GPL-2.0-only
+  license_family: GPL
+  license_file: LICENSE
+  summary: Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs
+  doc_url: https://github.com/kehrlab/PopIns2
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
+  skip-lints:
+    - missing_hash
+    - uses_vcs_url
\ No newline at end of file
diff --git a/recipes/popins2/popins2.patch b/recipes/popins2/popins2.patch
new file mode 100644
index 0000000000000..a72f893818356
--- /dev/null
+++ b/recipes/popins2/popins2.patch
@@ -0,0 +1,34 @@
+diff --git i/Makefile w/Makefile
+index de28bc8..613fa79 100644
+--- i/Makefile
++++ w/Makefile
+@@ -6,7 +6,7 @@ SRCS := $(shell find $(SRC_DIR) -type f -name *.cpp)
+ OBJS := $(patsubst $(SRC_DIR)/%,$(BUILD_DIR)/%,$(SRCS:.cpp=.o))
+ 
+ # Compiler
+-CXX = g++ -std=c++14
++CXX ?= g++ -std=c++14
+ CC = $(CXX)
+ 
+ # SeqAn
+@@ -29,7 +29,7 @@ CXXFLAGS += -march=native -DMAX_KMER_SIZE=64
+ CXXFLAGS += -I$(SEQAN_LIB)
+ 
+ # Linker flags
+-LDLIBS = -lbifrost -pthread -lz -rdynamic -DMAX_KMER_SIZE=64
++LDLIBS = -L"${PREFIX}/lib" -lbifrost -pthread -lz -rdynamic -DMAX_KMER_SIZE=64
+ # MacOS users might have to comment out the next line
+ LDLIBS += -lrt
+ 
+diff --git i/src/Traceback.h w/src/Traceback.h
+index 745db68..6323e80 100644
+--- i/src/Traceback.h
++++ w/src/Traceback.h
+@@ -6,6 +6,7 @@
+ #ifndef TRACEBACK_
+ #define TRACEBACK_
+ 
++#include <cstdint>
+ #include <iostream>
+ #include <fstream>
+