Merge pull request #20217 from smoors/20240326170611_new_pr_bwa-mem2221

{bio}[intel-compilers/2023.1.0] bwa-mem2 v2.2.1

easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1-intel-compilers-2023.1.0.eb

@@ -0,0 +1,37 @@
+easyblock = 'MakeCp'
+
+name = 'bwa-mem2'
+version = '2.2.1'
+
+homepage = 'https://github.com/bwa-mem2/bwa-mem2'
+description = """
+The tool bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It
+produces alignment identical to bwa and is ~1.3-3.1x faster depending on the
+use-case, dataset and the running machine."""
+
+toolchain = {'name': 'intel-compilers', 'version': '2023.1.0'}
+toolchainopts = {'pic': True, 'oneapi': False}
+
+github_account = 'bwa-mem2'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+patches = ['%(name)s-%(version)s_use_external_deps.patch']
+checksums = [
+    {'v2.2.1.tar.gz': '36ddd28ce7020d5a036ddeffa00e692296fd40c80380671bd4ea5757bd28841b'},
+    {'bwa-mem2-2.2.1_use_external_deps.patch': '0a9d7f7b3289029e19cf7dbab1778448097b9e0f92fa41a74a8cf81c9e114967'},
+]
+
+dependencies = [('safestringlib', '20240228')]
+
+build_cmd_targets = 'multi'
+
+files_to_copy = [(['bwa-mem2*'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/%(name)s'],
+    'dirs': [],
+}
+
+sanity_check_commands = ['bwa-mem2 version']
+
+moduleclass = 'bio'

easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1_use_external_deps.patch

@@ -0,0 +1,62 @@
+Use external safestringlib dependency
+Author: Samuel Moors (Vrije Universiteit Brussel)
+
+diff -ur bwa-mem2-2.2.1.orig/Makefile bwa-mem2-2.2.1/Makefile
+--- bwa-mem2-2.2.1.orig/Makefile	2021-03-17 06:36:00.000000000 +0100
++++ bwa-mem2-2.2.1/Makefile	2024-03-27 20:54:40.532807000 +0100
+@@ -42,14 +42,13 @@
+ ARCH_FLAGS=	-msse -msse2 -msse3 -mssse3 -msse4.1
+ MEM_FLAGS=	-DSAIS=1
+ CPPFLAGS+=	-DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 $(MEM_FLAGS) 
+-INCLUDES=   -Isrc -Iext/safestringlib/include
+-LIBS=		-lpthread -lm -lz -L. -lbwa -Lext/safestringlib -lsafestring $(STATIC_GCC)
++INCLUDES=   -Isrc
++LIBS=		-lpthread -lm -lz -L. -lbwa -lsafestring_shared $(STATIC_GCC)
+ OBJS=		src/fastmap.o src/bwtindex.o src/utils.o src/memcpy_bwamem.o src/kthread.o \
+ 			src/kstring.o src/ksw.o src/bntseq.o src/bwamem.o src/profiling.o src/bandedSWA.o \
+ 			src/FMI_search.o src/read_index_ele.o src/bwamem_pair.o src/kswv.o src/bwa.o \
+ 			src/bwamem_extra.o src/kopen.o
+ BWA_LIB=    libbwa.a
+-SAFE_STR_LIB=    ext/safestringlib/libsafestring.a
+
+ ifeq ($(arch),sse41)
+ 	ifeq ($(CXX), icpc)
+@@ -101,31 +100,27 @@
+ all:$(EXE)
+
+ multi:
+-	rm -f src/*.o $(BWA_LIB); cd ext/safestringlib/ && $(MAKE) clean;
++	rm -f src/*.o $(BWA_LIB);
+ 	$(MAKE) arch=sse41    EXE=bwa-mem2.sse41    CXX=$(CXX) all
+-	rm -f src/*.o $(BWA_LIB); cd ext/safestringlib/ && $(MAKE) clean;
++	rm -f src/*.o $(BWA_LIB);
+ 	$(MAKE) arch=sse42    EXE=bwa-mem2.sse42    CXX=$(CXX) all
+-	rm -f src/*.o $(BWA_LIB); cd ext/safestringlib/ && $(MAKE) clean;
++	rm -f src/*.o $(BWA_LIB);
+ 	$(MAKE) arch=avx    EXE=bwa-mem2.avx    CXX=$(CXX) all
+-	rm -f src/*.o $(BWA_LIB); cd ext/safestringlib/ && $(MAKE) clean;
++	rm -f src/*.o $(BWA_LIB);
+ 	$(MAKE) arch=avx2   EXE=bwa-mem2.avx2     CXX=$(CXX) all
+-	rm -f src/*.o $(BWA_LIB); cd ext/safestringlib/ && $(MAKE) clean;
++	rm -f src/*.o $(BWA_LIB);
+ 	$(MAKE) arch=avx512 EXE=bwa-mem2.avx512bw CXX=$(CXX) all
+-	$(CXX) -Wall -O3 src/runsimd.cpp -Iext/safestringlib/include -Lext/safestringlib/ -lsafestring $(STATIC_GCC) -o bwa-mem2
++	$(CXX) -Wall -O3 src/runsimd.cpp -lsafestring_shared $(STATIC_GCC) -o bwa-mem2
+
+
+-$(EXE):$(BWA_LIB) $(SAFE_STR_LIB) src/main.o
++$(EXE):$(BWA_LIB) src/main.o
+ 	$(CXX) $(CXXFLAGS) $(LDFLAGS) src/main.o $(BWA_LIB) $(LIBS) -o $@
+
+ $(BWA_LIB):$(OBJS)
+ 	ar rcs $(BWA_LIB) $(OBJS)
+
+-$(SAFE_STR_LIB):
+-	cd ext/safestringlib/ && $(MAKE) clean && $(MAKE) CC=$(CC) directories libsafestring.a
+-
+ clean:
+ 	rm -fr src/*.o $(BWA_LIB) $(EXE) bwa-mem2.sse41 bwa-mem2.sse42 bwa-mem2.avx bwa-mem2.avx2 bwa-mem2.avx512bw
+-	cd ext/safestringlib/ && $(MAKE) clean
+
+ depend:
+ 	(LC_ALL=C; export LC_ALL; makedepend -Y -- $(CXXFLAGS) $(CPPFLAGS) -I. -- src/*.cpp)

easybuild/easyconfigs/s/safestringlib/safestringlib-20240228-intel-compilers-2023.1.0.eb

@@ -0,0 +1,39 @@
+easyblock = 'CMakeMake'
+
+name = 'safestringlib'
+version = '20240228'
+_commit = 'b006356'
+
+homepage = 'https://github.com/intel/safestringlib'
+description = """
+The Secure Development Lifecycle (SDL) recommends banning certain C Library
+functions because they directly contribute to security vulnerabilities such as
+buffer overflows. However routines for the manipulation of strings and memory
+buffers are common in software and firmware, and are essential to accomplish
+certain programming tasks. Safer replacements for these functions that avoid or
+prevent serious security vulnerabilities (e.g. buffer overflows, string format
+attacks, conversion overflows/underflows, etc.) are available in the SafeString
+Library."""
+
+toolchain = {'name': 'intel-compilers', 'version': '2023.1.0'}
+
+github_account = 'intel'
+sources = [{
+    'source_urls': [GITHUB_SOURCE],
+    'download_filename': '%s.tar.gz' % _commit,
+    'filename': SOURCE_TAR_GZ,
+}]
+checksums = ['ea8e8952d7ade32a19df18af3a645ea54af924ff63a9b1a0b60e0e51be396d31']
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+]
+
+postinstallcmds = ['cp libsafestring_static.a %(installdir)s/lib/']
+
+sanity_check_paths = {
+    'files': ['lib/libsafestring_shared.%s' % SHLIB_EXT, 'lib/libsafestring_static.a'],
+    'dirs': ['include', 'share/safestring/cmake'],
+}
+
+moduleclass = 'lib'