{bio}[GCC/13.3.0] msisensor-pro 1.3.0

easybuild/easyconfigs/m/msisensor-pro/msisensor-pro-1.3.0-GCC-13.3.0.eb

@@ -0,0 +1,46 @@
+easyblock = 'MakeCp'
+
+name = 'msisensor-pro'
+version = '1.3.0'
+
+homepage = 'https://github.com/xjtu-omics/msisensor-pro/wiki'
+description = """MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with
+ next generation sequencing data. It accepts the whole genome sequencing, whole exome sequencing and
+ target region (panel) sequencing data as input."""
+
+toolchain = {'name': 'GCC', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/xjtu-omics/msisensor-pro/archive/refs/tags']
+sources = [{
+    'download_filename': 'v%(version)s.tar.gz',
+    'filename': SOURCE_TAR_GZ,
+}]
+patches = ['msisensor-pro-1.3.0_makefile.patch']
+checksums = [
+    {'msisensor-pro-1.3.0.tar.gz': '30d03841abfe12daee57984bb97687222534b18aeaa17ff7f4d1116dc31cc9c1'},
+    {'msisensor-pro-1.3.0_makefile.patch': '368ff680ab409532cb204c6b828bf5ca57d8a827e952e87a4fbbe440881b657b'},
+]
+
+dependencies = [
+    ('HTSlib', '1.21'),
+    ('bzip2', '1.0.8'),
+    ('ncurses', '6.5'),
+    ('zlib', '1.3.1'),
+]
+
+prebuildopts = 'cd cpp && '
+
+files_to_copy = [
+    (['binary/%(name)s-v%(version)s'],  'bin')
+]
+
+postinstallcmds = ["chmod +x %(installdir)s/bin/%(name)s-v%(version)s"]
+
+sanity_check_paths = {
+    'files': ['bin/%(name)s-v%(version)s'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["%(name)s-v%(version)s --help 2>&1 | grep 'Version: v%(version)s'"]
+
+moduleclass = 'bio'

easybuild/easyconfigs/m/msisensor-pro/msisensor-pro-1.3.0_makefile.patch

@@ -0,0 +1,48 @@
+Use Easybuild HTSlib
+author: John Dey [email protected]
+diff -ruN msisensor-pro-1.3.0.org/cpp/makefile msisensor-pro-1.3.0/cpp/makefile
+--- msisensor-pro-1.3.0.org/cpp/makefile	2024-09-27 00:13:58.000000000 -0700
++++ msisensor-pro-1.3.0/cpp/makefile	2025-01-14 16:10:12.006926000 -0800
+@@ -1,34 +1,30 @@
+ CXX=g++
+
+-HTSLIB=$(realpath ../vendor/htslib-1.11)
+ # HTSLIB_CPPFLAGS=-I$(realpath $(HTSLIB_ROOT))
+ # echo $(HTSLIB_CPPFLAGS)
+ # HTSLIB_LDFLAGS=-L/mnt/project/Project_Pindel/pindel_update/pindel/htslib/ -Wl,-rpath
+ CPP_ROOT=cpp
+ CXXFLAGS+=    -O2 -fopenmp
+-LDFLAGS+=    -L${HTSLIB}
+-INCLUDES+=    -I${HTSLIB}
++LDFLAGS := $(LDFLAGS)
++INCLUDES :=  $(INCLUDES)
+ LIBS+=    -lm -lz -lpthread -lhts
+-LD_LIBRARY_PATH+= -L${HTSLIB}
+-export LD_LIBRARY_PATH=${HTSLIB_ROOT}
++# LD_LIBRARY_PATH+= -L${HTSLIB}
++# export LD_LIBRARY_PATH=${HTSLIB_ROOT}
+
+ SOURCE = cmds scan distribution refseq polyscan param utilities homo window bamreader sample chi somatic
+ OBJS= $(patsubst %,%.o,$(SOURCE))
+
+ %.o:%.cpp
+-	        $(CXX) -L ${HTSLIB} -std=c++11 $(CXXFLAGS) $(INCLUDES) -c $< -o $@
++	$(CXX) -std=c++11 $(CXXFLAGS) $(LDFLAGS) $(INCLUDES) -c $< -o $@
+
+-all: htsfile msisensor-pro
+-#
+-htsfile:
+-	        $(MAKE) -C ${HTSLIB}
++all: msisensor-pro
+
+ msisensor-pro: $(OBJS)
+-	        $(CXX)  -std=c++11 $^ $(CXXFLAGS) $(LDFLAGS)  $(LIBS) -Wl,-rpath=${HTSLIB} -o $@
++	$(CXX)  -std=c++11 $^ $(CXXFLAGS) $(LDFLAGS)  $(LIBS) -o $@
+ 		# 	        $(CXX)  -std=c++11 $^ $(CXXFLAGS) $(INCLUDES)  $(LDFLAGS) $(LIBS) -o $@
+
+ clean:
+-	        rm -f *.o msisensor-pro
++	rm -f *.o msisensor-pro
+ 			        $(MAKE) -C ${HTSLIB}  clean
+
+