#470 working emmax_binary

470_emmax/emmax.eb

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+easyblock = 'MakeCp'
+
+name = 'EMMAX'
+# version is based on datestamp of files in emmax-beta-src.tar.gz
+# (last checked on 13 Aug 2024)
+version = '20120210'
+
+homepage = 'https://csg.sph.umich.edu//kang/emmax'
+description = """EMMAX is a statistical test for large scale human or model organism
+  association mapping accounting for the sample structure"""
+
+toolchain = {'name': 'intel', 'version': '2023b'}
+# https://csg.sph.umich.edu/kang/emmax/download/emmax-beta-intel.tar.gz
+source_urls = ['https://csg.sph.umich.edu//kang/emmax/download/']
+sources = [{'download_filename': 'emmax-beta-intel.tar.gz', 'filename': f'{name}-{version}-intel.tar.gz'}]
+checksums = ['d40a30b520f65d27cea6c47a8612d24a6e975a4b59623d3b23965d5a8e1755f5']
+
+# patches = ['EMMAX-20100310_fix-build.patch']
+
+dependencies = [
+    ('zlib', '1.2.13'),
+]
+
+# buildopts = 'CC="$CC $CFLAGS" CLIBS="-lflexiblas -lm -lz"'
+
+files_to_copy = [(['emmax', 'emmax-kin'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/emmax', 'bin/emmax-kin'],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    "emmax 2>&1 | grep '^Usage: emmax'",
+    "emmax-kin 2>&1 | grep '^Usage: emmax_IBS_kin'",
+]
+
+moduleclass = 'bio'
+
+# $EBROOTINTELMINCOMPILERS

470_emmax/emmax_binary.eb

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+easyblock = 'Binary'
+
+name = 'EMMAX'
+
+version = '20120210'
+versionsuffix = '-intel-binary'
+
+homepage = 'https://csg.sph.umich.edu/kang/emmax'
+description = """EMMAX is a statistical test for large scale human or model organism
+  association mapping accounting for the sample structure"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://csg.sph.umich.edu//kang/emmax/download/']
+sources = [
+    {
+        'download_filename': 'emmax-intel-binary-20120210.tar.gz',
+        'filename': f'{name}-{version}-intel-binary.tar.gz'
+    }
+]
+checksums = ['e2a582851ba1be908757d4ef436e98ad76664a0c55e00d13e55fa35fe2ba54dd']
+
+dependencies = [
+    ('zlib', '1.2.13'),
+]
+
+extract_sources = True
+
+sanity_check_paths = {
+    'files': ['emmax-intel64', 'emmax-kin-intel64'],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    "emmax-intel64 2>&1 | grep '^Usage: emmax'",
+    "emmax-kin-intel64 2>&1 | grep '^Usage: emmax_kin'",
+]
+
+moduleclass = 'bio'

470_emmax/patch1_buildsh/build.sh

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+# export INTELROOT=/home/hmkang/intel/Compiler/11.1/069
+export MKLROOT=${INTELROOT}/mkl
+export MKLINCLUDE=${MKLROOT}/include
+
+sh $INTELROOT/bin/iccvars.sh intel64
+sh $MKLROOT/tools/environment/mklvars64.sh
+export MKLLIBPATH=${MKLROOT}/lib/em64t
+export INTELLIBPATH=${INTELROOT}/lib/intel64
+export BINPATH=${INTELROOT}/bin/intel64
+
+$BINPATH/icc -Wall -wd1419 -O2 -I $MKLINCLUDE emmax-kin.c -Wl,--start-group $MKLLIBPATH/libmkl_intel_lp64.a $MKLLIBPATH/libmkl_intel_thread.a $MKLLIBPATH/libmkl_core.a $INTELLIBPATH/libguide.a -Wl,--end-group -lpthread -lz -o emmax-kin-intel64
+
+$BINPATH/icc -Wall -wd1419 -wd1418 -wd869 -wd920 -wd981 -wd1572 -O2 -I $MKLINCLUDE emmax.c -Wl,--start-group $MKLLIBPATH/libmkl_intel_lp64.a $MKLLIBPATH/libmkl_intel_thread.a $MKLLIBPATH/libmkl_core.a $INTELLIBPATH/libguide.a -Wl,--end-group -lpthread -lz -o emmax-intel64
+
+$BINPATH/icc -Wall -wd1419 -wd1418 -wd869 -wd920 -wd981 -wd1572 -O2 -I $MKLINCLUDE emmax-predict.cc -Wl,--start-group $MKLLIBPATH/libmkl_intel_lp64.a $MKLLIBPATH/libmkl_intel_thread.a $MKLLIBPATH/libmkl_core.a $INTELLIBPATH/libguide.a -Wl,--end-group -lpthread -lz -o emmax-predict-intel64

470_emmax/patch1_buildsh/build.sh.orig

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+export INTELROOT=/home/hmkang/intel/Compiler/11.1/069
+export MKLROOT=${INTELROOT}/mkl
+export MKLINCLUDE=${MKLROOT}/include
+
+sh $INTELROOT/bin/iccvars.sh intel64
+sh $MKLROOT/tools/environment/mklvars64.sh
+export MKLLIBPATH=${MKLROOT}/lib/em64t
+export INTELLIBPATH=${INTELROOT}/lib/intel64
+export BINPATH=${INTELROOT}/bin/intel64
+
+$BINPATH/icc -Wall -wd1419 -O2 -I $MKLINCLUDE emmax-kin.c -Wl,--start-group $MKLLIBPATH/libmkl_intel_lp64.a $MKLLIBPATH/libmkl_intel_thread.a $MKLLIBPATH/libmkl_core.a $INTELLIBPATH/libguide.a -Wl,--end-group -lpthread -lz -o emmax-kin-intel64
+
+$BINPATH/icc -Wall -wd1419 -wd1418 -wd869 -wd920 -wd981 -wd1572 -O2 -I $MKLINCLUDE emmax.c -Wl,--start-group $MKLLIBPATH/libmkl_intel_lp64.a $MKLLIBPATH/libmkl_intel_thread.a $MKLLIBPATH/libmkl_core.a $INTELLIBPATH/libguide.a -Wl,--end-group -lpthread -lz -o emmax-intel64
+
+$BINPATH/icc -Wall -wd1419 -wd1418 -wd869 -wd920 -wd981 -wd1572 -O2 -I $MKLINCLUDE emmax-predict.cc -Wl,--start-group $MKLLIBPATH/libmkl_intel_lp64.a $MKLLIBPATH/libmkl_intel_thread.a $MKLLIBPATH/libmkl_core.a $INTELLIBPATH/libguide.a -Wl,--end-group -lpthread -lz -o emmax-predict-intel64