From 9fda22d942854098bc48bec4256456957d5005e8 Mon Sep 17 00:00:00 2001
From: snehring <7978778+snehring@users.noreply.github.com>
Date: Mon, 25 Sep 2023 23:26:19 -0500
Subject: bcl2fastq2: patch for compiling on aarch64 (#40195)

---
 .../builtin/packages/bcl2fastq2/cxxConfigure-aarch64.patch    | 11 +++++++++++
 var/spack/repos/builtin/packages/bcl2fastq2/package.py        |  2 ++
 2 files changed, 13 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/bcl2fastq2/cxxConfigure-aarch64.patch

diff --git a/var/spack/repos/builtin/packages/bcl2fastq2/cxxConfigure-aarch64.patch b/var/spack/repos/builtin/packages/bcl2fastq2/cxxConfigure-aarch64.patch
new file mode 100644
index 0000000000..490b9fcd07
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bcl2fastq2/cxxConfigure-aarch64.patch
@@ -0,0 +1,11 @@
+--- a/src/cmake/cxxConfigure.cmake      2017-06-22 12:14:50.000000000 -0500
++++ b/src/cmake/cxxConfigure.cmake      2023-09-25 11:50:55.819690648 -0500
+@@ -118,7 +118,7 @@
+ set(BCL2FASTQ_DEP_LIB ${BCL2FASTQ_DEP_LIB} "${LIBEXSLT_LIBRARIES}" "${LIBXSLT_LIBRARIES}" "${LIBXML2_LIBRARIES}")
+
+ #set (CMAKE_CXX_FLAGS "$ENV{CXX_FLAGS} $ENV{CXXFLAGS} -fopenmp -msse2 -Werror -Wall -Wextra -Wunused -Wno-long-long -Wsign-compare -Wpointer-arith" CACHE STRING "g++ flags" FORCE)
+-set (CMAKE_CXX_FLAGS "$ENV{CXX_FLAGS} $ENV{CXXFLAGS} -std=c++11 -fopenmp -msse2 -Wall -Wextra -Wunused -Wno-long-long -Wsign-compare -Wpointer-arith" CACHE STRING "g++ flags" FORCE)
++set (CMAKE_CXX_FLAGS "$ENV{CXX_FLAGS} $ENV{CXXFLAGS} -std=c++11 -fopenmp -Wall -Wextra -Wunused -Wno-long-long -Wsign-compare -Wpointer-arith" CACHE STRING "g++ flags" FORCE)
+ #set (CMAKE_CXX_FLAGS_DEBUG "-O0 -g -pg -fprofile-arcs -ftest-coverage -D_GLIBCXX_DEBUG" CACHE STRING "g++ flags" FORCE)
+ set (CMAKE_CXX_FLAGS_DEBUG "-O0 -std=c++11 -g -pg -fprofile-arcs -ftest-coverage" CACHE STRING "g++ flags" FORCE)
+ #set (CMAKE_CXX_FLAGS_DEBUG "-std=c++11 -O0 -g -pg -fprofile-arcs -ftest-coverage" CACHE STRING "g++ flags" FORCE)
diff --git a/var/spack/repos/builtin/packages/bcl2fastq2/package.py b/var/spack/repos/builtin/packages/bcl2fastq2/package.py
index 2dfc2ac8e5..65695f04f4 100644
--- a/var/spack/repos/builtin/packages/bcl2fastq2/package.py
+++ b/var/spack/repos/builtin/packages/bcl2fastq2/package.py
@@ -49,6 +49,8 @@ class Bcl2fastq2(Package):
     # After finding the libxslt bits, cmake still needs to wire in the
     # libexslt bits.
     patch("cxxConfigure-cmake.patch")
+    # -msse2 isn't valid for arm
+    patch("cxxConfigure-aarch64.patch", when="target=aarch64:")
 
     root_cmakelists_dir = "src"
 
-- 
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