From 4d91d8d560eb58986c0572ef12ef2a53bb02bd18 Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>
Date: Sat, 17 Nov 2018 02:27:21 +0100
Subject: [PATCH] Fix octopus binary "invalid instruction" (-march too new)
 (#11822)

* This attempts to make the binary more portable by only requiring Sandybridge.

* Fix march set to native
---
 recipes/octopus/fix_march_set_to_native.patch | 12 ++++++++++++
 recipes/octopus/meta.yaml                     |  4 +++-
 2 files changed, 15 insertions(+), 1 deletion(-)
 create mode 100644 recipes/octopus/fix_march_set_to_native.patch

diff --git a/recipes/octopus/fix_march_set_to_native.patch b/recipes/octopus/fix_march_set_to_native.patch
new file mode 100644
index 0000000000000..b6ab6a8885dce
--- /dev/null
+++ b/recipes/octopus/fix_march_set_to_native.patch
@@ -0,0 +1,12 @@
+diff -rNu octopus-0.5.2-beta.orig/src/CMakeLists.txt octopus-0.5.2-beta/src/CMakeLists.txt
+--- octopus-0.5.2-beta.orig/src/CMakeLists.txt	2018-10-29 08:36:32.000000000 -0600
++++ octopus-0.5.2-beta/src/CMakeLists.txt	2018-11-13 15:54:06.000000000 -0700
+@@ -639,7 +639,7 @@
+ else()
+     add_executable(octopus main.cpp ${OCTOPUS_SOURCES} ${INCLUDE_SOURCES})
+     target_compile_features(octopus PRIVATE cxx_thread_local)
+-    target_compile_options(octopus PRIVATE -ffast-math -funroll-loops -march=native)
++    target_compile_options(octopus PRIVATE -ffast-math -funroll-loops)
+     target_include_directories(octopus PUBLIC ${octopus_SOURCE_DIR}/lib ${octopus_SOURCE_DIR}/src)
+     target_link_libraries(octopus tandem ranger)
+     if (NOT BUILD_SHARED_LIBS)
diff --git a/recipes/octopus/meta.yaml b/recipes/octopus/meta.yaml
index 36a6a4f081dd3..50cc2b6b726e7 100644
--- a/recipes/octopus/meta.yaml
+++ b/recipes/octopus/meta.yaml
@@ -7,7 +7,7 @@ package:
   version: {{ version }}
 
 build:
-  number: 0
+  number: 1
   # Not building on osx CircleCI and unsure how to fix; does not pick
   # up 7.2 compilers
   skip: true # [osx]
@@ -15,6 +15,8 @@ build:
 source:
   url: https://github.com/luntergroup/{{ name }}/archive/v0.5.2-beta.tar.gz
   sha256: {{ sha256 }}
+  patches:
+    - fix_march_set_to_native.patch
 
 requirements:
   build: