From 7acfc7a62c4b8fa215f4d22dff73254f04dca4a5 Mon Sep 17 00:00:00 2001
From: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Date: Fri, 13 Dec 2024 15:38:03 +0200
Subject: [PATCH] Add recipe for softsv

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
---
 recipes/softsv/build.sh       | 10 ++++++++
 recipes/softsv/makefile.patch | 13 +++++++++++
 recipes/softsv/meta.yaml      | 43 +++++++++++++++++++++++++++++++++++
 3 files changed, 66 insertions(+)
 create mode 100644 recipes/softsv/build.sh
 create mode 100644 recipes/softsv/makefile.patch
 create mode 100644 recipes/softsv/meta.yaml

diff --git a/recipes/softsv/build.sh b/recipes/softsv/build.sh
new file mode 100644
index 0000000000000..217a7aa6ed8cb
--- /dev/null
+++ b/recipes/softsv/build.sh
@@ -0,0 +1,10 @@
+#!/usr/bin/env bash
+
+set -xe
+
+CXX="${CXX} -std=c++14" make -j"${CPU_COUNT}"
+
+ls -la
+
+mkdir -p ${PREFIX}/bin
+install -m 755 softsv ${PREFIX}/bin
diff --git a/recipes/softsv/makefile.patch b/recipes/softsv/makefile.patch
new file mode 100644
index 0000000000000..e6125c5cc4302
--- /dev/null
+++ b/recipes/softsv/makefile.patch
@@ -0,0 +1,13 @@
+diff --git i/Makefile w/Makefile
+index de28bc8..e352ed0 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
diff --git a/recipes/softsv/meta.yaml b/recipes/softsv/meta.yaml
new file mode 100644
index 0000000000000..7920bbec6f4ba
--- /dev/null
+++ b/recipes/softsv/meta.yaml
@@ -0,0 +1,43 @@
+{% set name = "softsv" %}
+{% set version = "1.4.2" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage(name, max_pin='x') }}
+
+source:
+  url: https://sourceforge.net/projects/{{ name }}/files/SoftSV_{{ version }}.zip
+  sha256: b3caea962569f7c30f1257ad148fd1e833f8d0737105b9983579d91da2bed6e8
+  patches:
+    - softsv.patch
+
+requirements:
+  build:
+    - make
+    - {{ compiler('cxx') }}
+  host:
+    - boost-cpp
+    - bamtools
+    - seqan
+
+test:
+  commands:
+    - ls -la # temporary
+
+about:
+  home: https://sourceforge.net/projects/softsv
+  license: GPL-3.0-only
+  license_family: GPL3
+  license_file: license.txt
+  summary: SoftSV is a tool for the detection of small and large deletions, inversions, tandem duplications and translocations from paired-end sequencing data.
+  doc_url: https://sourceforge.net/projects/softsv
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
\ No newline at end of file